[med-svn] [Git][med-team/prokka][upstream] New upstream version 1.14.5+dfsg
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Nov 23 16:56:07 GMT 2019
Michael R. Crusoe pushed to branch upstream at Debian Med / prokka
Commits:
2537477a by Michael R. Crusoe at 2019-11-23T16:34:22Z
New upstream version 1.14.5+dfsg
- - - - -
19 changed files:
- .gitignore
- .travis.yml
- README.md
- bin/prokka
- bin/prokka-abricate_to_fasta_db
- + db/cm/Archaea
- db/cm/Bacteria
- db/cm/README
- db/cm/Viruses
- + db/cm/__build/.gitignore
- + db/cm/__build/Rfam_archaea_14.1.txt
- + db/cm/__build/Rfam_bacteria_14.1.txt
- + db/cm/__build/Rfam_viruses_14.1.txt
- + db/cm/__build/archaea.sql
- + db/cm/__build/bacteria.sql
- + db/cm/__build/update.sh
- + db/cm/__build/viruses.sql
- − doc/prokka-manual.txt
- − doc/update_manual.sh
Changes:
=====================================
.gitignore
=====================================
@@ -17,7 +17,6 @@ nytprof.out
pm_to_blib
bug/
db/cm/*.i1*
-db/kingdom/*/sprot.p*
+db/kingdom/*/*.p??
db/hmm/*.h3?
db/genus/*.p*
-
=====================================
.travis.yml
=====================================
@@ -1,7 +1,5 @@
language: perl
-sudo: false
-
perl:
- "5.26"
=====================================
README.md
=====================================
@@ -1,4 +1,7 @@
-[](https://travis-ci.org/tseemann/prokka) [](https://www.gnu.org/licenses/gpl-3.0) [](#lang-au) [](https://doi.org/10.1093/bioinformatics/btu153) 
+[](https://travis-ci.org/tseemann/prokka)
+[](https://www.gnu.org/licenses/gpl-3.0)
+[](https://doi.org/10.1093/bioinformatics/btu153)
+
# Prokka: rapid prokaryotic genome annotation
@@ -50,7 +53,7 @@ $HOME/prokka/bin/prokka --setupdb
## Test
-* Type `prokka` and it should output it's help screen.
+* Type `prokka` and it should output its help screen.
* Type `prokka --version` and you should see an output like `prokka 1.x`
* Type `prokka --listdb` and it will show you what databases it has installed to use.
@@ -133,9 +136,11 @@ $HOME/prokka/bin/prokka --setupdb
-g linear -c PROK -n 11 -f PRJEB12345/EHEC-Chr1.embl \
"Escherichia coli" 562 PRJEB12345 "Escherichia coli strain EHEC" PRJEB12345/EHEC-Chr1.gff
-# Download and run the EMBL validator prior to submitting the EMBL flat file
-% curl -L -O ftp://ftp.ebi.ac.uk/pub/databases/ena/lib/embl-client.jar
-% java -jar embl-client.jar -r PRJEB12345/EHEC-Chr1.embl
+# Download and run the latest EMBL validator prior to submitting the EMBL flat file
+# from http://central.maven.org/maven2/uk/ac/ebi/ena/sequence/embl-api-validator/
+# which at the time of writing is v1.1.129
+% curl -L -O http://central.maven.org/maven2/uk/ac/ebi/ena/sequence/embl-api-validator/1.1.129/embl-api-validator-1.1.129.jar
+% java -jar embl-api-validator-1.1.129.jar -r PRJEB12345/EHEC-Chr1.embl
# Compress the file ready to upload to ENA, and calculate MD5 checksum
% gzip PRJEB12345/EHEC-Chr1.embl
@@ -178,7 +183,6 @@ $HOME/prokka/bin/prokka --setupdb
General:
--help This help
--version Print version and exit
- --docs Show full manual/documentation
--citation Print citation for referencing Prokka
--quiet No screen output (default OFF)
--debug Debug mode: keep all temporary files (default OFF)
@@ -205,6 +209,7 @@ $HOME/prokka/bin/prokka --setupdb
Annotations:
--kingdom [X] Annotation mode: Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria')
--gcode [N] Genetic code / Translation table (set if --kingdom is set) (default '0')
+ --prodigaltf [X] Prodigal training file (default '')
--gram [X] Gram: -/neg +/pos (default '')
--usegenus Use genus-specific BLAST databases (needs --genus) (default OFF)
--proteins [X] Fasta file of trusted proteins to first annotate from (default '')
@@ -235,6 +240,13 @@ use of Genbank is recommended over FASTA, because it will provide `/gene`
and `/EC_number` annotations that a typical `.faa` file will not provide, unless
you have specially formatted it for Prokka.
+### Option: --prodigaltf
+
+Instead of letting `prodigal` train its gene model on the contigs you
+provide, you can pre-train it on some good closed reference genomes first
+using the `prodigal -t` option. Once you've done that, provide `prokka`
+the training file using the `--prodgialtf` option.
+
### Option: --rawproduct
Prokka annotates proteins by using sequence similarity to other proteins in its database,
@@ -262,11 +274,20 @@ BLAST+. This combination of small database and fast search typically
completes about 70% of the workload. Then a series of slower but more
sensitive HMM databases are searched using HMMER3.
-The initial core databases are derived from UniProtKB; there is one per
-"kingdom" supported. To qualify for inclusion, a protein must be (1) from
-Bacteria (or Archaea or Viruses); (2) not be "Fragment" entries; and (3)
-have an evidence level ("PE") of 2 or lower, which corresponds to
-experimental mRNA or proteomics evidence.
+The three core databases, applied in order, are:
+
+1. [ISfinder](https://isfinder.biotoul.fr/):
+Only the tranposase (protein) sequences; the whole transposon is not annotated.
+
+2. [NCBI Bacterial Antimicrobial Resistance Reference Gene Database](https://www.ncbi.nlm.nih.gov/bioproject/313047):
+Antimicrobial resistance genes curated by NCBI.
+
+3. [UniProtKB (SwissProt)](https://www.uniprot.org/uniprot/?query=reviewed:yes):
+For each `--kingdom` we include curated proteins with evidence that
+(i) from Bacteria (or Archaea or Viruses);
+(ii) not be "Fragment" entries;
+and (iii) have an evidence level ("PE") of 2 or lower, which
+corresponds to experimental mRNA or proteomics evidence.
#### Making a Core Databases
@@ -278,6 +299,8 @@ has been detected properly.
#### The Genus Databases
+:warning: This is no longer recommended. Please use `--proteins` instead.
+
If you enable `--usegenus` and also provide a Genus via `--genus` then it
will first use a BLAST database which is Genus specific. Prokka comes with
a set of databases for the most common Bacterial genera; type prokka
@@ -366,7 +389,7 @@ There is no clear reason for this. The only way to restore normal behaviour
is to edit the prokka script and change `parallel` to `parallel --gnu`.
* __Why does prokka fail when it gets to hmmscan?__
-Unfortunately HMMER keeps changing it's database format, and they aren't
+Unfortunately HMMER keeps changing its database format, and they aren't
upward compatible. If you upgraded HMMER (from 3.0 to 3.1 say) then you
need to "re-press" the files. This can be done as follows:
```
@@ -388,6 +411,11 @@ compliant. It does not like the ACCESSION and VERSION strings that Prokka
produces via the "tbl2asn" tool. The following Unix command will fix them:
`egrep -v '^(ACCESSION|VERSION)' prokka.gbk > mauve.gbk`
+* __How can I make my GFF not have the contig sequences in it?__
+```
+sed '/^##FASTA/Q' prokka.gff > nosequence.gff
+```
+
## Bugs
Submit problems or requests to the [Issue Tracker](https://github.com/tseemann/prokka/issues).
=====================================
bin/prokka
=====================================
@@ -23,11 +23,12 @@ use warnings;
use FindBin;
use Cwd qw(abs_path);
use File::Copy;
+use File::Basename;
use Time::Piece;
use Time::Seconds;
use XML::Simple;
use Digest::MD5;
-use List::Util qw(min max sum);
+use List::Util qw(min max sum uniq);
use Scalar::Util qw(openhandle);
use Data::Dumper;
use Bio::Root::Version;
@@ -45,7 +46,7 @@ my @CMDLINE = ($0, @ARGV);
my $OPSYS = $^O;
my $BINDIR = "$FindBin::RealBin/../binaries/$OPSYS";
my $EXE = $FindBin::RealScript;
-my $VERSION = "1.14.0";
+my $VERSION = "1.14.5";
my $AUTHOR = 'Torsten Seemann <torsten.seemann at gmail.com>';
my $URL = 'https://github.com/tseemann/prokka';
my $PROKKA_PMID = '24642063';
@@ -104,7 +105,7 @@ my %tools = (
NEEDED => 0,
},
'barrnap' => {
- GETVER => "barrnap --version 2>&1",
+ GETVER => "LC_ALL=C barrnap --version 2>&1",
REGEXP => qr/($BIDEC)/,
MINVER => "0.4",
NEEDED => 0,
@@ -113,12 +114,11 @@ my %tools = (
GETVER => "prodigal -v 2>&1 | grep -i '^Prodigal V'",
REGEXP => qr/($BIDEC)/,
MINVER => "2.6",
- MAXVER => "2.69", # changed cmdline options in 2.70 git :-/
NEEDED => 1,
},
'signalp' => {
# this is so long-winded as -v changed meaning (3.0=version, 4.0=verbose !?)
- GETVER => "signalp -v < /dev/null 2>&1 | egrep ',|# SignalP' | sed 's/^# SignalP-//'",
+ GETVER => "if [ \"`signalp -version 2>&1 | grep -Eo '[0-9]+\.[0-9]+'`\" != \"\" ]; then echo `signalp -version 2>&1 | grep -Eo '[0-9]+\.[0-9]+'`; else signalp -v < /dev/null 2>&1 | egrep ',|# SignalP' | sed 's/^# SignalP-//'; fi",
REGEXP => qr/^($BIDEC)/,
MINVER => "3.0",
NEEDED => 0, # only if --gram used
@@ -172,7 +172,6 @@ my %tools = (
NEEDED => 1,
},
# now just the standard unix tools we need
- 'less' => { NEEDED=>1 },
'grep' => { NEEDED=>1 }, # yes, we need this before we can test versions :-/
'egrep' => { NEEDED=>1 },
'sed' => { NEEDED=>1 },
@@ -185,6 +184,12 @@ my %tools = (
# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
# functions to check if tool is installed and correct version
+sub ver2str {
+ my($bidec) = @_;
+ return $bidec if $bidec !~ m/\./;
+ return join '', map { sprintf "%03d",$_ } (split m/\./, $bidec);
+}
+
sub check_tool {
my($toolname) = @_;
my $t = $tools{$toolname};
@@ -196,19 +201,17 @@ sub check_tool {
if ($t->{GETVER}) {
my($s) = qx($t->{GETVER});
if (defined $s) {
- $s =~ $t->{REGEXP};
- $t->{VERSION} = $1 if defined $1;
- msg("Determined $toolname version is $t->{VERSION}");
- if (defined $t->{MINVER} and $t->{VERSION} < $t->{MINVER}) {
+ chomp $s;
+ $s =~ $t->{REGEXP} or err("Coult not parse version from '$s'");;
+ $t->{VERSION} = ver2str($1);
+ msg("Determined $toolname version is $t->{VERSION} from '$s'");
+ if (defined $t->{MINVER} and $t->{VERSION} lt ver2str($t->{MINVER}) ) {
err("Prokka needs $toolname $t->{MINVER} or higher. Please upgrade and try again.");
}
- if (defined $t->{MAXVER} and $t->{VERSION} > $t->{MAXVER}) {
- err("Prokka needs a version of $toolname between $t->{MINVER} and $t->{MAXVER}. Please downgrade and try again.");
- }
}
else {
err("Could not determine version of $toolname - please install version",
- $t->{MINVER}, "or higher"); # FIXME: or less <= MAXVER if given
+ $t->{MINVER}, "or higher");
}
}
}
@@ -227,7 +230,7 @@ sub check_all_tools {
my(@Options, $quiet, $debug, $kingdom, $fast, $force, $outdir, $prefix, $cpus, $dbdir,
$addgenes, $addmrna, $cds_rna_olap,
$gcode, $gram, $gffver, $locustag, $increment, $mincontiglen, $evalue, $coverage,
- $genus, $species, $strain, $plasmid,
+ $genus, $species, $strain, $plasmid, $prodigaltf,
$usegenus, $proteins, $hmms, $centre, $scaffolds,
$rfam, $norrna, $notrna, $rnammer, $rawproduct, $noanno, $accver,
$metagenome, $compliant, $listdb, $citation);
@@ -621,29 +624,31 @@ if ($rfam) {
my $num_ncrna = 0;
my $tool = "Infernal:".$tools{'cmscan'}->{VERSION};
my $icpu = $cpus || 1;
- my $cmd = "cmscan --rfam --cpu $icpu -E $evalue --tblout /dev/stdout -o /dev/null --noali $cmdb \Q$outdir/$prefix.fna\E";
+ my $dbsize = $total_bp * 2 / 1000000;
+ my $cmd = "cmscan -Z $dbsize --cut_ga --rfam --nohmmonly --fmt 2 --cpu $icpu --tblout /dev/stdout -o /dev/null --noali $cmdb \Q$outdir/$prefix.fna\E";
msg("Running: $cmd");
open INFERNAL, '-|', $cmd;
while (<INFERNAL>) {
next if m/^#/; # ignore comments
my @x = split ' '; # magic Perl whitespace splitter
- # msg("DEBUG: ", join("~~~", @x) );
- next unless @x > 9; # avoid incorrect lines
- next unless defined $x[1] and $x[1] =~ m/^RF\d/;
- my $sid = $x[2];
+ next unless defined $x[2] and $x[2] =~ m/^RF\d/;
+ my $sid = $x[3];
next unless exists $seq{$sid};
+ next if defined $x[19] and $x[19] =~ m/^=$/; # Overlaps with a higher scoring match
push @{$seq{$sid}{FEATURE}}, Bio::SeqFeature::Generic->new(
-primary => 'misc_RNA',
-seq_id => $sid,
-source => $tool,
- -start => min($x[7], $x[8]),
- -end => max($x[7], $x[8]),
- -strand => ($x[9] eq '-' ? -1 : +1),
- -score => undef, # possibly x[16] but had problems here with '!'
+ -start => min($x[9], $x[10]),
+ -end => max($x[9], $x[10]),
+ -strand => ($x[11] eq '-' ? -1 : +1),
+ -score => $x[16],
-frame => 0,
-tag => {
- 'product' => $x[0],
+ 'product' => $x[1],
'inference' => "COORDINATES:profile:$tool",
+ 'accession' => $x[2],
+ 'Note' => '"' . join(' ', @x[26..$#x]) . '"',
}
);
$num_ncrna++;
@@ -710,6 +715,10 @@ my $prodigal_mode = ($totalbp >= 100000 && !$metagenome) ? 'single' : 'meta';
msg("Contigs total $totalbp bp, so using $prodigal_mode mode");
my $num_cds=0;
my $cmd = "prodigal -i \Q$outdir/$prefix.fna\E -c -m -g $gcode -p $prodigal_mode -f sco -q";
+if ($prodigaltf and -r $prodigaltf) {
+ msg("Gene finding will be aided by Prodigal training file: $prodigaltf");
+ $cmd .= " -t '$prodigaltf'";
+}
msg("Running: $cmd");
open my $PRODIGAL, '-|', $cmd;
my $sid;
@@ -774,14 +783,15 @@ for my $sid (@seq) {
# Find signal peptide leader sequences
if ($tools{signalp}->{HAVE}) {
- my $sigpver = substr $tools{signalp}{VERSION}, 0, 1; # first char, expect 3 or 4
+ my $sigpver = substr $tools{signalp}{VERSION}, 0, 1; # first char, expect 3, 4 or 5
- if ($kingdom eq 'Bacteria' and $sigpver==3 || $sigpver==4) {
+ if ($kingdom eq 'Bacteria' and $sigpver==3 || $sigpver==4 || $sigpver==5) {
if ($gram) {
$gram = $gram =~ m/\+|[posl]/i ? 'gram+' : 'gram-';
msg("Looking for signal peptides at start of predicted proteins");
msg("Treating $kingdom as $gram");
my $spoutfn = "$outdir/signalp.faa";
+ my $sp5outfn = "$outdir/signalp_summary.signalp5";
open my $spoutfh, '>', $spoutfn;
my $spout = Bio::SeqIO->new(-fh=>$spoutfh, -format=>'fasta');
my %cds;
@@ -800,12 +810,17 @@ if ($tools{signalp}->{HAVE}) {
msg("Skipping signalp because it can not handle >$SIGNALP_MAXSEQ sequences.");
}
else {
- my $opts = $sigpver==3 ? '-m hmm' : '';
- my $cmd = "signalp -t $gram -f short $opts \Q$spoutfn\E 2> /dev/null";
+ my $opts = $sigpver==3 ? "signalp -t $gram -f short -m hmm" : ($sigpver==4 ? "signalp -t $gram -f short" : '$(which signalp)'." -tmp $outdir -prefix $outdir/signalp -org $gram -format short -fasta");
+ my $cmd = "$opts \Q$spoutfn\E 2> /dev/null";
msg("Running: $cmd");
my $tool = "SignalP:".$tools{signalp}->{VERSION};
my $num_sigpep = 0;
- open SIGNALP, '-|', $cmd;
+ if ($sigpver == 3 or $sigpver == 4) {
+ open SIGNALP, '-|', $cmd;
+ } else {
+ qx($cmd);
+ open SIGNALP, '<', $sp5outfn;
+ }
while (<SIGNALP>) {
my @x = split m/\s+/;
if ($sigpver == 3) {
@@ -834,8 +849,7 @@ if ($tools{signalp}->{HAVE}) {
);
push @{$seq{$parent->seq_id}{FEATURE}}, $sigpep;
$num_sigpep++;
- }
- else {
+ } elsif ($sigpver == 4) {
# msg("sigp$sigpver: @x");
next unless @x==12 and $x[9] eq 'Y'; # has sig_pep
my $parent = $cds{ $x[0] };
@@ -861,11 +875,45 @@ if ($tools{signalp}->{HAVE}) {
);
push @{$seq{$parent->seq_id}{FEATURE}}, $sigpep;
$num_sigpep++;
- }
+ } else {
+ # msg("sigp$sigpver: @x");
+ next unless @x==12 and $x[1] =~ m/^SP|TAT|LIPO/; # has sig_pep
+ my $parent = $cds{ $x[0] };
+ my $tpprob;
+ if ($x[1] =~ m/^SP/) { $tpprob = $x[2] }
+ elsif ($x[1] =~ m/^TAT/) { $tpprob = $x[3] }
+ elsif ($x[1] =~ m/^LIPO/) { $tpprob = $x[4] }
+ my $type = "$x[1] (Probability: $tpprob)";
+ my ($cleave1, $cleave2) = ($1, $2) if $x[8] =~ m/(\d+)-(\d+)\./;
+ my $cleaveseq = $1 if $x[9] =~ m/(\w+-\w+)\./;
+ my $clprob = $x[11];
+ my $start = $parent->strand > 0 ? $parent->start : $parent->end;
+ # need to convert to DNA coordinates
+ my $end = $start + $parent->strand * ($cleave1*3 - 1);
+ my $sigpep = Bio::SeqFeature::Generic->new(
+ -seq_id => $parent->seq_id,
+ -source_tag => $tool,
+ -primary => 'sig_peptide',
+ -start => min($start, $end),
+ -end => max($start, $end),
+ -strand => $parent->strand,
+ -frame => 0, # PHASE: compulsory for peptides, can't be '.'
+ -tag => {
+ # 'ID' => $ID,
+ # 'Parent' => $x[0], # don't have proper IDs yet....
+ 'product' => "putative signal peptide",
+ 'inference' => "ab initio prediction:$tool",
+ 'note' => "$type, predicted cleavage between residues $cleave1 and $cleave2 ($cleaveseq) with probability $clprob",
+ }
+ );
+ push @{$seq{$parent->seq_id}{FEATURE}}, $sigpep;
+ $num_sigpep++;
+ }
}
msg("Found $num_sigpep signal peptides");
}
delfile($spoutfn);
+ delfile($sp5outfn) if $sigpver == 5;
}
else {
msg("Option --gram not specified, will NOT check for signal peptides.");
@@ -1017,8 +1065,7 @@ else {
}
# create a unqiue output name so we can save them in --debug mode
- my $outname = $db->{DB};
- $outname =~ s{^.*/}{};
+ my $outname = "$prefix.".basename($db->{DB}).".tmp.$$";
# we write out all the CDS which haven't been annotated yet and then search them
my $faa_name = "$outdir/$outname.faa";
@@ -1263,7 +1310,7 @@ for my $sid (@seq) {
$fsa_fh->write_seq($ctg);
$ctg->desc(undef);
print $tbl_fh ">Feature $sid\n";
- for my $f ( sort { $a->start <=> $b->start } @{ $seq{$sid}{FEATURE} }) {
+ for my $f ( sort { $a->start <=> $b->start || $b->end <=> $a->end || $a->has_tag('Parent') <=> $b->has_tag('Parent') } @{ $seq{$sid}{FEATURE} }) {
if ($f->primary_tag eq 'CDS' and not $f->has_tag('product')) {
$f->add_tag_value('product', $HYPO);
}
@@ -1527,13 +1574,6 @@ sub version {
#----------------------------------------------------------------------
-sub showdoc {
- system("less $FindBin::Bin/../doc/$EXE-manual.txt");
- exit;
-}
-
-#----------------------------------------------------------------------
-
sub show_citation {
print STDERR << "EOCITE";
@@ -1567,7 +1607,7 @@ sub add_bundle_to_path {
#----------------------------------------------------------------------
sub kingdoms {
- return map { m{kingdom/(\w+?)/}; $1 } glob("$dbdir/kingdom/*/*.pin");
+ return uniq map { m{kingdom/(\w+?)/}; $1 } glob("$dbdir/kingdom/*/*.pin");
}
sub genera {
@@ -1622,7 +1662,7 @@ sub setup_db {
}
check_tool('cmpress');
- for my $cm (<$dbdir/cm/{Viruses,Bacteria}>) {
+ for my $cm (<$dbdir/cm/{Viruses,Bacteria,Archaea}>) {
msg("Pressing CM database: $cm");
runcmd("cmpress \Q$cm\E");
}
@@ -1691,7 +1731,6 @@ sub setOptions {
'General:',
{OPT=>"help", VAR=>\&usage, DESC=>"This help"},
{OPT=>"version", VAR=>\&version, DESC=>"Print version and exit"},
- {OPT=>"docs", VAR=>\&showdoc, DESC=>"Show full manual/documentation"},
{OPT=>"citation",VAR=>\&show_citation, DESC=>"Print citation for referencing Prokka"},
{OPT=>"quiet!", VAR=>\$quiet, DEFAULT=>0, DESC=>"No screen output"},
{OPT=>"debug!", VAR=>\$debug, DEFAULT=>0, DESC=>"Debug mode: keep all temporary files"},
@@ -1722,6 +1761,7 @@ sub setOptions {
'Annotations:',
{OPT=>"kingdom=s", VAR=>\$kingdom, DEFAULT=>'Bacteria', DESC=>"Annotation mode: ".join('|', kingdoms()) },
{OPT=>"gcode=i", VAR=>\$gcode, DEFAULT=>0, DESC=>"Genetic code / Translation table (set if --kingdom is set)"},
+ {OPT=>"prodigaltf=s", VAR=>\$prodigaltf, DEFAULT=>'', DESC=>"Prodigal training file" },
{OPT=>"gram=s", VAR=>\$gram, DEFAULT=>'', DESC=>"Gram: -/neg +/pos"},
{OPT=>"usegenus!", VAR=>\$usegenus, DEFAULT=>0, DESC=>"Use genus-specific BLAST databases (needs --genus)"},
{OPT=>"proteins=s", VAR=>\$proteins, DEFAULT=>'', DESC=>"FASTA or GBK file to use as 1st priority"},
=====================================
bin/prokka-abricate_to_fasta_db
=====================================
@@ -24,12 +24,20 @@ my $out = Bio::SeqIO->new(-fh=>\*STDOUT, -format=>'fasta');
my %seen;
while (my $seq = $in->next_seq) {
- my(undef,$gene,$locustag) = split m"~~~", $seq->id;
- $gene = '' if $gene eq $locustag;
+ my(undef,$gene,$acc,$abx) = split m"~~~", $seq->id;
+ $gene = '' if $gene eq $acc;
my $prot = $seq->translate;
- die Dumper($prot) if $prot->seq =~ m/\*./; # check for stop codon in middle
- die Dumper($prot) if $seen{$prot->seq}++; # check for dupes
- $prot->id($locustag);
+ my $aa = $prot->seq;
+ die Dumper($prot) if $aa =~ m/\*./; # check for stop codon in middle
+ die Dumper($prot) if $seen{$aa}++; # check for dupes
+ substr($aa,0,1) = "M"; # force Met start
+ chop($aa) if $aa =~ m/\*$/; # remove trailing stop codon
+ $prot->seq($aa);
+ $prot->id($acc);
+ # 1. no /EC_number
+ # 2. /gene
+ # 3. /product
+ # 4. COG
$prot->desc( join('~~~', '', $gene, $prot->desc, '') );
$out->write_seq($prot);
}
=====================================
db/cm/Archaea
=====================================
Binary files /dev/null and b/db/cm/Archaea differ
=====================================
db/cm/Bacteria
=====================================
Binary files a/db/cm/Bacteria and b/db/cm/Bacteria differ
=====================================
db/cm/README
=====================================
@@ -1,29 +1,27 @@
-The .cm files in this folder were generated by extracting only those RFAM entries that
-had members from the Bacteria and Viruses divisions (based on their taxonomy ID in the .gff3 file)
+The .cm files in this folder were generated by extracting only those Rfam entries that
+had members from the Bacteria, Viruses, and Archaea divisions (based on their taxonomy
+description in the public Rfam MySQL database).
-Archaea had no entries, so we just use Bacteria.
+For more details, see the __build/ directory and https://github.com/tseemann/prokka/issues/243.
-- 523 #=GF TP Gene; miRNA; # microRNA - euk only?
-- 421 #=GF TP Gene; snRNA; snoRNA; CD-box; # Small nucleolar RNAs
-+ 252 #=GF TP Gene; sRNA; #
-- 225 #=GF TP Gene; snRNA; snoRNA; HACA-box; Small nucleolar RNAs
-- 225 #=GF TP Gene; lncRNA; # Long non-coding RNAs > 200 bp
-+ 218 #=GF TP Cis-reg;
-+ 87 #=GF TP Gene;
-+ 65 #=GF TP Gene; CRISPR;
-+ 28 #=GF TP Cis-reg; frameshift_element;
-+ 27 #=GF TP Cis-reg; IRES;
-+ 26 #=GF TP Cis-reg; riboswitch;
-+ 23 #=GF TP Gene; antisense;
-- 18 #=GF TP Gene; snRNA; snoRNA; scaRNA;
-+ 15 #=GF TP Gene; ribozyme;
-- 11 #=GF TP Gene; snRNA; splicing;
-+ 11 #=GF TP Cis-reg; leader;
-+ 10 #=GF TP Intron;
-+ 7 #=GF TP Cis-reg; thermoregulator;
-- 6 #=GF TP Gene; rRNA; # rnammer
-+ 5 #=GF TP Gene; antitoxin;
-- 3 #=GF TP Gene; snRNA;
-- 2 #=GF TP Gene; tRNA; # aragorn
+$ for file in __build/Rfam_*_14.1.txt; do tail -n +2 $file; done | cut -f 2 | sort | uniq -c | sort -rn
+ 723 Gene; sRNA;
+ 279 Cis-reg;
+ 68 Gene; CRISPR;
+ 62 Gene; antisense;
+ 60 Gene; snRNA; snoRNA; CD-box;
+ 57 Gene;
+ 48 Cis-reg; riboswitch;
+ 39 Gene; miRNA;
+ 34 Cis-reg; leader;
+ 33 Cis-reg; thermoregulator;
+ 26 Cis-reg; frameshift_element;
+ 21 Intron;
+ 21 Gene; ribozyme;
+ 18 Gene; snRNA; snoRNA; HACA-box;
+ 12 Gene; antitoxin;
+ 11 Cis-reg; IRES;
+ 2 Gene; snRNA;
+ 1 Gene; snRNA; snoRNA; HACA-box
=====================================
db/cm/Viruses
=====================================
Binary files a/db/cm/Viruses and b/db/cm/Viruses differ
=====================================
db/cm/__build/.gitignore
=====================================
@@ -0,0 +1,2 @@
+*.cm
+Rfam.cm.gz
=====================================
db/cm/__build/Rfam_archaea_14.1.txt
=====================================
@@ -0,0 +1,152 @@
+RF00010 Gene; ribozyme; Bacterial RNase P class A
+RF00017 Gene; Metazoan signal recognition particle RNA
+RF00028 Intron; Group I catalytic intron
+RF00029 Intron; Group II catalytic intron
+RF00030 Gene; ribozyme; RNase MRP
+RF00032 Cis-reg; Histone 3' UTR stem-loop
+RF00050 Cis-reg; riboswitch; FMN riboswitch (RFN element)
+RF00058 Gene; snRNA; snoRNA; HACA-box; HgcF RNA (Pab35)
+RF00059 Cis-reg; riboswitch; TPP riboswitch (THI element)
+RF00060 Gene; snRNA; snoRNA; HACA-box; HgcE RNA (Pab105)
+RF00062 Gene; HgcC family RNA
+RF00063 Gene; SscA RNA
+RF00064 Gene; snRNA; snoRNA; HACA-box HgcG RNA (Pab40)
+RF00065 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA snoR9
+RF00095 Gene; snRNA; snoRNA; CD-box; Pyrococcus C/D box small nucleolar RNA
+RF00150 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA SNORD42
+RF00169 Gene; Bacterial small signal recognition particle RNA
+RF00174 Cis-reg; riboswitch; Cobalamin riboswitch
+RF00373 Gene; ribozyme; Archaeal RNase P
+RF00380 Cis-reg; riboswitch; ykoK leader
+RF00504 Cis-reg; riboswitch; Glycine riboswitch
+RF00517 Cis-reg; leader; serC leader
+RF00845 Gene; miRNA; microRNA MIR158
+RF01051 Cis-reg; Cyclic di-GMP-I riboswitch
+RF01068 Cis-reg; Guanidine-II riboswitch
+RF01119 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR32
+RF01120 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR33
+RF01121 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR38
+RF01122 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR39
+RF01123 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR35
+RF01124 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR36
+RF01125 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR4
+RF01126 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR41
+RF01127 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR42
+RF01128 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR42
+RF01129 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR44
+RF01130 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR46
+RF01131 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR47
+RF01132 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR48
+RF01133 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR3
+RF01134 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR30
+RF01135 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR24
+RF01136 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR28
+RF01137 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR21
+RF01138 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR23
+RF01139 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR2
+RF01140 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR20
+RF01141 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR18
+RF01142 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR19
+RF01143 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR16
+RF01144 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR17
+RF01145 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR14
+RF01146 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR15
+RF01147 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR12
+RF01149 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR10
+RF01150 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR11
+RF01152 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR1
+RF01273 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR34
+RF01274 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR45
+RF01275 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR22
+RF01276 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR53
+RF01297 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR40
+RF01303 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR49
+RF01304 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR5
+RF01305 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR51
+RF01306 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR52
+RF01307 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR55
+RF01308 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR58
+RF01309 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR60
+RF01310 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR7
+RF01312 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR9
+RF01319 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01320 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01322 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01324 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01326 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01328 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01337 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01338 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01339 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01350 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01351 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01353 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01354 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01355 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01358 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01360 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01369 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01373 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01375 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01377 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01378 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01380 Cis-reg; Human immunodeficiency virus type 1 major splice donor
+RF01419 Gene; antisense; Antisense RNA which regulates isiA expression
+RF01689 Cis-reg; riboswitch; AdoCbl variant RNA
+RF01717 Cis-reg; PhotoRC-II RNA
+RF01722 Gene; sRNA; Pyrobac-1 RNA
+RF01725 Cis-reg; riboswitch; SAM-I/IV variant riboswitch
+RF01734 Cis-reg; riboswitch; Fluoride riboswitch
+RF01737 Cis-reg; flpD RNA
+RF01745 Cis-reg; manA RNA
+RF01761 Cis-reg; wcaG RNA
+RF01829 Gene; snRNA; snoRNA; CD-box; sR6 snoRNA
+RF01854 Gene; Bacterial large signal recognition particle RNA
+RF01856 Gene; Protozoan signal recognition particle RNA
+RF01857 Gene; Archaeal signal recognition particle RNA
+RF01982 Cis-reg; Pyrrolysine insertion sequence 1
+RF01998 Intron; Group II catalytic intron D1-D4-1
+RF01999 Intron; Group II catalytic intron D1-D4-2
+RF02001 Intron; Group II catalytic intron D1-D4-3
+RF02003 Intron; Group II catalytic intron D1-D4-4
+RF02005 Intron; Group II catalytic intron D1-D4-6
+RF02012 Intron; Group II catalytic intron D1-D4-7
+RF02033 Gene; HNH endonuclease-associated RNA and ORF (HEARO) RNA
+RF02163 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR-tMet
+RF02194 Gene; antisense; Bacterial antisense RNA HPnc0260
+RF02253 Cis-reg; Iron response element II
+RF02276 Gene; ribozyme; Hammerhead ribozyme (type II)
+RF02357 Gene; ribozyme; RNaseP truncated form
+RF02509 Cis-reg; Pyrrolysine insertion sequence mtbB
+RF02510 Cis-reg; Pyrrolysine insertion sequence mttB
+RF02511 Cis-reg; Pyrrolysine insertion sequence TetR
+RF02512 Cis-reg; Pyrrolysine insertion sequence transposase 1
+RF02513 Cis-reg; Pyrrolysine insertion sequence transposase 2
+RF02514 Gene; sRNA; 5' ureB small RNA
+RF02656 Gene; sRNA; Sense overlapping transcript RNA 0042 (sot)
+RF02657 Gene; sRNA; Sense overlapping transcript RNA 2652 (sot)
+RF02792 Gene; antisense; Archaeal Small RNA 162
+RF02794 Gene; snRNA; snoRNA; HACA-box; Pab19 RNA
+RF02795 Gene; snRNA; snoRNA; HACA-box; Pab91 RNA
+RF02796 Gene; snRNA; snoRNA; HACA-box; Pab160 RNA
+RF02800 Gene; sRNA; Rickettsia sRNA47
+RF02801 Gene; snRNA; snoRNA; HACA-box; Pyrobaculum sRNA 201
+RF02802 Gene; snRNA; snoRNA; HACA-box; Pyrobaculum sRNA 204
+RF02803 Gene; snRNA; snoRNA; HACA-box; Pyrobaculum sRNA 205
+RF02804 Gene; snRNA; snoRNA; HACA-box; Pyrobaculum sRNA 206
+RF02805 Gene; snRNA; snoRNA; HACA-box; Pyrobaculum sRNA 207
+RF02806 Gene; snRNA; snoRNA; HACA-box; Pyrobaculum sRNA 208
+RF02807 Gene; snRNA; snoRNA; HACA-box; Pyrobaculum sRNA 209
+RF02808 Gene; snRNA; snoRNA; HACA-box; Pyrobaculum sRNA 210
+RF02814 Gene; sRNA; Sulfolobus sRNA133
+RF02820 Gene; antisense; Vibrio RNA AS9
+RF02905 Gene; sRNA; Archaeal Small RNA 41
+RF02906 Gene; sRNA; Archaeal Small RNA 154
+RF02914 Cis-reg; DUF805b RNA
+RF02921 Gene; sRNA; RT-14 RNA
+RF02984 Gene; sRNA; DUF3800-X RNA
+RF02996 Gene; sRNA; int-alpA RNA
+RF03001 Cis-reg; leuA-Halobacteria RNA
+RF03006 Gene; sRNA; M23 RNA
+RF03019 Gene; sRNA; RT-16 RNA
+RF03094 Gene; sRNA; LAGLIDADG-2 RNA
=====================================
db/cm/__build/Rfam_bacteria_14.1.txt
=====================================
@@ -0,0 +1,1127 @@
+RF00008 Gene; ribozyme; Hammerhead ribozyme (type III)
+RF00010 Gene; ribozyme; Bacterial RNase P class A
+RF00011 Gene; ribozyme; Bacterial RNase P class B
+RF00012 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA U3
+RF00013 Gene; 6S / SsrS RNA
+RF00014 Gene; sRNA; DsrA RNA
+RF00017 Gene; Metazoan signal recognition particle RNA
+RF00018 Gene; sRNA; CsrB/RsmB RNA family
+RF00021 Gene; sRNA; Spot 42 RNA
+RF00022 Gene; GcvB RNA
+RF00028 Intron; Group I catalytic intron
+RF00029 Intron; Group II catalytic intron
+RF00032 Cis-reg; Histone 3' UTR stem-loop
+RF00033 Gene; antisense; MicF RNA
+RF00034 Gene; sRNA; RprA RNA
+RF00035 Gene; sRNA; OxyS RNA
+RF00038 Cis-reg; thermoregulator; PrfA thermoregulator UTR
+RF00039 Gene; antisense; DicF RNA
+RF00040 Cis-reg; RNase E 5' UTR element
+RF00042 Gene; antisense; CopA-like RNA
+RF00043 Gene; antisense; R1162-like plasmid antisense RNA
+RF00049 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA SNORD36
+RF00050 Cis-reg; riboswitch; FMN riboswitch (RFN element)
+RF00057 Gene; sRNA; RyhB RNA
+RF00059 Cis-reg; riboswitch; TPP riboswitch (THI element)
+RF00066 Gene; snRNA; U7 small nuclear RNA
+RF00077 Gene; sRNA; SraB RNA
+RF00078 Gene; sRNA; MicA sRNA
+RF00079 Gene; sRNA; OmrA-B family
+RF00080 Cis-reg; riboswitch; yybP-ykoY manganese riboswitch
+RF00081 Gene; sRNA; ArcZ RNA
+RF00082 Gene; sRNA; SraG RNA
+RF00083 Gene; sRNA; GlmZ RNA activator of glmS mRNA
+RF00084 Gene; sRNA; CsrC RNA family
+RF00101 Gene; sRNA; SraC/RyeA RNA
+RF00104 Gene; miRNA; mir-10 microRNA precursor family
+RF00106 Gene; antisense; RNAI
+RF00107 Gene; FinP
+RF00109 Cis-reg; Vimentin 3' UTR protein-binding region
+RF00110 Gene; sRNA; RybB RNA
+RF00111 Gene; sRNA; SdsR_RyeB RNA
+RF00112 Gene; sRNA; CyaR/Rye RNA
+RF00113 Gene; antitoxin; Short Intergenic Abundant RNA
+RF00114 Cis-reg; leader; Ribosomal S15 leader
+RF00115 Gene; sRNA; McaS/IsrA RNA
+RF00116 Gene; sRNA; C0465 RNA
+RF00117 Gene; sRNA; C0719 RNA
+RF00118 Gene; sRNA; rydB RNA
+RF00119 Gene; sRNA; C0299 RNA
+RF00121 Gene; sRNA; MicC RNA
+RF00122 Gene; sRNA; GadY
+RF00124 Gene; sRNA; IS102 RNA
+RF00125 Gene; sRNA; IS128 RNA
+RF00126 Gene; sRNA; ryfA RNA
+RF00127 Gene; sRNA; t44 RNA
+RF00128 Gene; sRNA; Glm Y RNA activator of glmS mRNA
+RF00140 Cis-reg; Alpha operon ribosome binding site
+RF00162 Cis-reg; riboswitch; SAM riboswitch (S box leader)
+RF00166 Gene; sRNA; PrrB/RsmZ RNA family
+RF00167 Cis-reg; riboswitch; Purine riboswitch
+RF00168 Cis-reg; riboswitch; Lysine riboswitch
+RF00169 Gene; Bacterial small signal recognition particle RNA
+RF00170 Gene; Retron msr RNA
+RF00174 Cis-reg; riboswitch; Cobalamin riboswitch
+RF00195 Gene; sRNA; RsmY RNA family
+RF00199 Gene; SL2 RNA
+RF00207 Cis-reg; K10 transport/localisation element (TLS)
+RF00210 Cis-reg; IRES; Aphthovirus internal ribosome entry site (IRES)
+RF00230 Cis-reg; leader; T-box leader
+RF00234 Cis-reg; riboswitch; glmS glucosamine-6-phosphate activated ribozyme
+RF00235 Gene; Plasmid RNAIII
+RF00236 Gene; antisense; ctRNA
+RF00238 Gene; antisense; ctRNA
+RF00240 Gene; antisense; RNA-OUT
+RF00241 Gene; miRNA; mir-8/mir-141/mir-200 microRNA precursor family
+RF00242 Gene; antisense; ctRNA
+RF00243 Cis-reg; traJ 5' UTR
+RF00250 Gene; miRNA; Trans-activation response element (TAR)
+RF00262 Gene; antisense; sar RNA
+RF00368 Gene; sRNA; sroB RNA
+RF00369 Gene; sRNA; sroC RNA
+RF00370 Gene; sRNA; sroD RNA
+RF00371 Gene; sRNA; sroE RNA
+RF00372 Gene; sRNA; sroH RNA
+RF00373 Gene; ribozyme; Archaeal RNase P
+RF00375 Cis-reg; HIV primer binding site (PBS)
+RF00378 Gene; sRNA; Qrr RNA
+RF00379 Cis-reg; riboswitch; ydaO/yuaA leader
+RF00380 Cis-reg; riboswitch; ykoK leader
+RF00382 Cis-reg; frameshift_element; DnaX ribosomal frameshifting element
+RF00383 Cis-reg; frameshift_element; Insertion sequence IS1222 ribosomal frameshifting element
+RF00388 Gene; antisense; Anti-Q RNA
+RF00391 Cis-reg; RtT RNA
+RF00392 Gene; snRNA; snoRNA; HACA-box; Small nucleolar RNA SNORA5
+RF00397 Gene; snRNA; snoRNA; HACA-box; Small nucleolar RNA SNORA14
+RF00435 Cis-reg; thermoregulator; Repression of heat shock gene expression (ROSE) element
+RF00442 Cis-reg; riboswitch; Guanidine-I riboswitch
+RF00444 Gene; sRNA; PrrF RNA
+RF00456 Gene; miRNA; mir-34 microRNA precursor family
+RF00485 Cis-reg; Potassium channel RNA editing signal
+RF00489 Gene; antisense; ctRNA
+RF00490 Cis-reg; S-element
+RF00503 Gene; RNAIII
+RF00504 Cis-reg; riboswitch; Glycine riboswitch
+RF00505 Gene; sRNA; RydC RNA
+RF00506 Cis-reg; leader; Threonine operon leader
+RF00512 Cis-reg; leader; Leucine operon leader
+RF00513 Cis-reg; leader; Tryptophan operon leader
+RF00514 Cis-reg; leader; Histidine operon leader
+RF00515 Cis-reg; PyrR binding site
+RF00516 Cis-reg; leader; ylbH leader
+RF00517 Cis-reg; leader; serC leader
+RF00518 Cis-reg; leader; speF leader
+RF00519 Gene; sRNA; Makes More Granules Regulator RNA (mmgR)
+RF00520 Cis-reg; leader; ybhL leader
+RF00521 Cis-reg; riboswitch; SAM riboswitch (alpha-proteobacteria)
+RF00522 Cis-reg; riboswitch; PreQ1 riboswitch
+RF00523 Cis-reg; Prion pseudoknot
+RF00534 Gene; antisense; SgrS RNA
+RF00552 Cis-reg; rncO
+RF00555 Cis-reg; leader; Ribosomal protein L13 leader
+RF00556 Cis-reg; leader; Ribosomal protein L19 leader
+RF00557 Cis-reg; leader; Ribosomal protein L10 leader
+RF00558 Cis-reg; leader; Ribosomal protein L20 leader
+RF00559 Cis-reg; leader; Ribosomal protein L21 leader
+RF00560 Gene; snRNA; snoRNA; HACA-box; Small nucleolar RNA SNORA17
+RF00598 Gene; snRNA; snoRNA; HACA-box; Small nucleolar RNA SNORA76
+RF00615 Gene; sRNA; Listeria Hfq binding LhrA
+RF00616 Gene; sRNA; Listeria LhrC
+RF00623 Gene; Pseudomonas sRNA P1
+RF00624 Gene; Pseudomonas sRNA P9
+RF00625 Gene; Pseudomonas sRNA P11
+RF00627 Gene; Pseudomonas sRNA P15
+RF00629 Gene; Pseudomonas sRNA P24
+RF00630 Gene; Pseudomonas sRNA P26
+RF00632 Cis-reg; sxy 5' UTR element
+RF00634 Cis-reg; riboswitch; S-adenosyl methionine (SAM) riboswitch,
+RF00655 Gene; miRNA; microRNA mir-28
+RF00660 Gene; miRNA; microRNA mir-214
+RF00722 Gene; miRNA; microRNA mir-451
+RF00782 Gene; miRNA; microRNA MIR480
+RF00804 Gene; miRNA; microRNA mir-240
+RF00824 Gene; miRNA; microRNA mir-50
+RF00828 Gene; miRNA; microRNA mir-75
+RF00843 Gene; miRNA; microRNA mir-228
+RF00845 Gene; miRNA; microRNA MIR158
+RF00846 Gene; miRNA; microRNA mir-64
+RF00848 Gene; miRNA; microRNA mir-61
+RF00857 Gene; miRNA; microRNA mir-233
+RF00882 Gene; miRNA; microRNA MIR811
+RF00892 Gene; miRNA; microRNA mir-551
+RF00898 Gene; miRNA; microRNA mir-242
+RF01016 Gene; miRNA; microRNA mir-584
+RF01031 Gene; miRNA; microRNA mir-639
+RF01051 Cis-reg; Cyclic di-GMP-I riboswitch
+RF01053 Gene; Deinococcus radiodurans Y RNA
+RF01054 Cis-reg; riboswitch; preQ1-II (pre queuosine) riboswitch
+RF01055 Cis-reg; riboswitch; Moco (molybdenum cofactor) riboswitch
+RF01056 Cis-reg; riboswitch; Magnesium Sensor
+RF01057 Cis-reg; riboswitch; S-adenosyl-L-homocysteine riboswitch
+RF01059 Gene; miRNA; microRNA mir-598
+RF01065 Cis-reg; 23S methyl RNA motif
+RF01066 Cis-reg; 6C RNA
+RF01067 Gene; ATPC RNA motif
+RF01068 Cis-reg; Guanidine-II riboswitch
+RF01069 Cis-reg; purD RNA motif
+RF01070 Cis-reg; SucA RNA motif
+RF01071 Gene; Ornate Large Extremophilic RNA
+RF01072 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01077 Cis-reg; Pseudoknot of tRNA-like structure
+RF01083 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01087 Cis-reg; Pseudoknot of the regulatory region of the repZ gene
+RF01089 Cis-reg; Pseudoknot of the regulatory region of the repBA gene
+RF01114 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01116 Gene; sRNA; Cyanobacterial functional RNA 1
+RF01131 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR47
+RF01133 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA sR3
+RF01197 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA snR39
+RF01262 Gene; snRNA; snoRNA; HACA-box; Small nucleolar RNA snR44
+RF01277 Gene; snRNA; snoRNA; CD-box; Small nucleolar RNA U54
+RF01315 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01316 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01317 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01318 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01320 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01321 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01322 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01323 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01325 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01327 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01329 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01330 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01331 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01332 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01333 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01334 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01335 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01336 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01339 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01340 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01341 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01342 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01343 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01344 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01345 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01346 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01347 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01348 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01349 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01352 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01353 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01356 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01357 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01359 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01361 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01362 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01363 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01364 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01365 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01366 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01367 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01368 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01370 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01371 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01374 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01376 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01379 Gene; CRISPR; CRISPR RNA direct repeat element
+RF01380 Cis-reg; Human immunodeficiency virus type 1 major splice donor
+RF01383 Gene; GRIK4 3 prime UTR element
+RF01384 Gene; Invasion gene-associated RNA
+RF01385 Gene; sRNA; isrA Hfq binding RNA
+RF01386 Gene; sRNA; isrB Hfq binding RNA
+RF01387 Gene; sRNA; isrC Hfq binding RNA
+RF01388 Gene; sRNA; isrD Hfq binding RNA
+RF01389 Gene; sRNA; isrF Hfq binding RNA
+RF01390 Gene; sRNA; isrG Hfq binding RNA
+RF01391 Gene; sRNA; isrH Hfq binding RNA
+RF01392 Gene; sRNA; isrI Hfq binding RNA
+RF01393 Gene; sRNA; isrJ Hfq binding RNA
+RF01394 Gene; sRNA; isrK Hfq binding RNA
+RF01395 Gene; sRNA; isrL Hfq binding RNA
+RF01396 Gene; sRNA; isrN Hfq binding RNA
+RF01397 Gene; sRNA; isrO Hfq binding RNA
+RF01398 Gene; sRNA; isrP Hfq binding RNA
+RF01399 Gene; sRNA; isrQ Hfq binding RNA
+RF01400 Gene; antitoxin; istR Hfq binding RNA
+RF01401 Gene; sRNA; rseX Hfq binding RNA
+RF01402 Gene; sRNA; STnc150 Hfq binding RNA
+RF01403 Gene; sRNA; STnc290 Hfq binding RNA
+RF01404 Gene; sRNA; PinT (STnc440) Hfq binding RNA
+RF01405 Gene; sRNA; STnc490 Hfq binding RNA
+RF01406 Gene; sRNA; STnc500 Hfq binding RNA
+RF01407 Gene; sRNA; STnc560 Hfq binding RNA
+RF01408 Gene; sRNA; sraL Hfq binding RNA
+RF01409 Gene; sRNA; STnc250 Hfq binding RNA
+RF01410 Gene; sRNA; BsrC
+RF01411 Gene; sRNA; BsrF
+RF01412 Gene; sRNA; BsrG
+RF01416 Gene; antisense; NrrF RNA
+RF01419 Gene; antisense; Antisense RNA which regulates isiA expression
+RF01456 Gene; antisense; Vibrio regulatory RNA of OmpA
+RF01457 Gene; sRNA; Listeria sRNA rli22
+RF01458 Gene; antisense; Listeria snRNA rli23
+RF01459 Gene; sRNA; Listeria sRNA rliE
+RF01460 Gene; sRNA; Listeria sRNA rliH
+RF01461 Gene; sRNA; Listeria sRNA rli22
+RF01462 Gene; sRNA; Listeria sRNA rli26
+RF01463 Gene; sRNA; Listeria sRNA rli27
+RF01464 Gene; sRNA; Listeria sRNA rliA
+RF01465 Gene; sRNA; Listeria sRNA rli31
+RF01466 Gene; sRNA; Listeria sRNA rli34
+RF01467 Gene; sRNA; Listeria sRNA rli36
+RF01468 Gene; sRNA; Listeria sRNA rli32
+RF01469 Gene; sRNA; Listeria sRNA rli33
+RF01470 Gene; sRNA; Listeria sRNA rli38
+RF01471 Gene; sRNA; Listeria sRNA rliB
+RF01472 Gene; sRNA; Listeria sRNA rli40
+RF01473 Gene; sRNA; Listeria sRNA rli41
+RF01474 Gene; sRNA; Listeia sRNA rli42
+RF01475 Gene; antisense; Listeria snRNA rli45
+RF01476 Gene; sRNA; Listeria sRNA rliF
+RF01477 Gene; sRNA; Listeria sRNA rli43
+RF01478 Gene; sRNA; Listeria sRNA rli47
+RF01479 Gene; sRNA; Listeria sRNA rli48
+RF01480 Cis-reg; Listeria sRNA rli52
+RF01481 Cis-reg; Listeria sRNA rli53
+RF01482 Cis-reg; riboswitch; AdoCbl riboswitch
+RF01483 Cis-reg; Listeria sRNA rli56
+RF01484 Cis-reg; Listeria sRNA rli59
+RF01485 Cis-reg; Listeria sRNA rli61
+RF01486 Cis-reg; Listeria sRNA rli62
+RF01487 Gene; sRNA; Listeria sRNA rliI
+RF01488 Gene; sRNA; Listeria sRNA rli49
+RF01489 Gene; sRNA; Listeria sRNA sbrA
+RF01490 Cis-reg; Listeria snRNA rli51
+RF01491 Cis-reg; Listeria sRNA rli54
+RF01492 Gene; sRNA; Listeria sRNA rli28
+RF01493 Gene; sRNA; Listeria sRNA rli37
+RF01494 Gene; antisense; Listeria sRNA rliD
+RF01497 Cis-reg; ALIL pseudoknot
+RF01510 Cis-reg; riboswitch; M. florum riboswitch
+RF01515 Gene; snRNA; snoRNA; CD-box; A. fumigatus snoRNA Afu_514
+RF01517 Cis-reg; iscR stability element
+RF01519 Gene; sRNA; Caulobacter sRNA CC0196
+RF01520 Gene; sRNA; caulobacter sRNA CC0734
+RF01521 Gene; sRNA; caulobacter sRNA CC1840
+RF01527 Gene; sRNA; Caulobacter sRNA CrfA
+RF01528 Gene; sRNA; caulobacter sRNA CC3513
+RF01529 Gene; sRNA; Cauldobacter sRNA CC3552
+RF01530 Gene; sRNA; Caulobacter sRNA CC3664
+RF01656 Gene; sRNA; Nematode sRNA ceN72-3_ceN74-2
+RF01665 Gene; sRNA; Pseudomonas sRNA P13
+RF01668 Gene; sRNA; Pseudomonas sRNA P10
+RF01669 Gene; sRNA; Pseudomonas sRNA P14
+RF01670 Gene; sRNA; Pseudomonas sRNA P17
+RF01671 Gene; sRNA; Pseudomonas sRNA P18
+RF01672 Gene; sRNA; Psudomonas sRNA P2
+RF01673 Gene; sRNA; PhrS
+RF01674 Gene; sRNA; Pseudomonas sRNA P27
+RF01675 Gene; sRNA; Pseudomonas sRNA CrcZ
+RF01676 Gene; sRNA; Pseudomonas sRNA P31
+RF01677 Gene; sRNA; Pseudomonas sRNA P35
+RF01678 Gene; sRNA; Pseudomonas sRNA P37
+RF01679 Gene; sRNA; Pseudomonas sRNA P36
+RF01680 Gene; sRNA; Pseudomonas sRNA P5
+RF01681 Gene; sRNA; Pseudomonas sRNA P4
+RF01682 Gene; sRNA; Pseudomonas sRNA P8
+RF01683 Gene; sRNA; Pseudomonas sRNA P6
+RF01685 Gene; sRNA; 6S-Flavo RNA
+RF01686 Gene; sRNA; Acido-1 RNA
+RF01687 Gene; sRNA; Acido-Lenti-1 RNA
+RF01688 Cis-reg; Actino-pnp RNA
+RF01689 Cis-reg; riboswitch; AdoCbl variant RNA
+RF01690 Gene; sRNA; Bacillaceae-1 RNA
+RF01691 Gene; sRNA; Bacillus-plasmid RNA
+RF01692 Cis-reg; leader; Bacteroidete tryptophan peptide leader RNA
+RF01693 Gene; sRNA; Bacteroidales-1 RNA
+RF01694 Gene; sRNA; Bacteroides-1 RNA
+RF01695 Gene; antisense; C4 antisense RNA
+RF01696 Gene; sRNA; Chlorobi-1 RNA
+RF01697 Cis-reg; Chlorobi-RRM RNA
+RF01698 Gene; sRNA; Chloroflexi-1 RNA
+RF01699 Gene; sRNA; Clostridiales-1 RNA
+RF01700 Gene; sRNA; Collinsella-1 RNA
+RF01701 Gene; sRNA; Cyano-1 RNA
+RF01702 Gene; sRNA; Cyano-2 RNA
+RF01703 Gene; sRNA; Dictyoglomi-1 RNA
+RF01704 Cis-reg; Downstream peptide RNA
+RF01705 Gene; sRNA; Flavo-1 RNA
+RF01706 Gene; sRNA; Gut-1 RNA
+RF01707 Cis-reg; JUMPstart RNA
+RF01708 Cis-reg; L17 ribosomal protein downstream element
+RF01709 Cis-reg; Lacto-rpoB RNA
+RF01710 Gene; sRNA; Lacto-usp RNA
+RF01711 Cis-reg; Lnt RNA
+RF01712 Gene; sRNA; Methylobacterium-1 RNA
+RF01713 Cis-reg; Moco-II RNA
+RF01715 Cis-reg; Pedo-repair RNA
+RF01716 Cis-reg; PhotoRC-I RNA
+RF01717 Cis-reg; PhotoRC-II RNA
+RF01718 Gene; sRNA; Polynucleobacter-1 RNA
+RF01719 Gene; sRNA; Pseudomon-1/ErsA RNA
+RF01720 Cis-reg; Pseudomon-Rho RNA
+RF01721 Cis-reg; Pseudomon-groES RNA
+RF01723 Gene; sRNA; Rhizobiales-2 RNA
+RF01724 Cis-reg; SAM-Chlorobi RNA
+RF01725 Cis-reg; riboswitch; SAM-I/IV variant riboswitch
+RF01726 Cis-reg; SAM-II long loop
+RF01727 Cis-reg; riboswitch; SAM/SAH riboswitch
+RF01728 Gene; sRNA; STAXI RNA
+RF01729 Cis-reg; Termite-flg RNA
+RF01731 Cis-reg; TwoAYGGAY RNA
+RF01732 Gene; sRNA; MarS sRNA
+RF01733 Cis-reg; atoC RNA
+RF01734 Cis-reg; riboswitch; Fluoride riboswitch
+RF01735 Cis-reg; epsC RNA
+RF01736 Cis-reg; flg-Rhizobiales RNA
+RF01738 Cis-reg; gabT RNA
+RF01739 Cis-reg; riboswitch; Glutamine riboswitch
+RF01740 Cis-reg; gyrA RNA
+RF01742 Gene; sRNA; lactis-plasmid RNA
+RF01743 Cis-reg; leader; leu/phe leader RNA from Lactococcus
+RF01744 Cis-reg; livK RNA
+RF01745 Cis-reg; manA RNA
+RF01746 Cis-reg; mraW RNA
+RF01747 Cis-reg; msiK RNA
+RF01748 Cis-reg; nuoG RNA
+RF01749 Cis-reg; pan motif
+RF01750 Cis-reg; riboswitch; ZMP/ZTP riboswitch
+RF01752 Cis-reg; psaA RNA
+RF01753 Cis-reg; psbNH RNA
+RF01754 Cis-reg; radC RNA
+RF01755 Cis-reg; rmf RNA
+RF01756 Cis-reg; rne-II RNA
+RF01757 Gene; sRNA; sbcD RNA
+RF01758 Cis-reg; sucA-II RNA
+RF01759 Cis-reg; sucC RNA
+RF01760 Cis-reg; traJ-II RNA
+RF01762 Gene; sRNA; Whalefall-1 RNA
+RF01763 Cis-reg; Guanidine-III riboswitch
+RF01764 Cis-reg; yjdF RNA
+RF01766 Cis-reg; thermoregulator; cspA thermoregulator
+RF01767 Cis-reg; riboswitch; SMK box translational riboswitch
+RF01769 Cis-reg; leader; Enterobacteria greA leader
+RF01770 Cis-reg; leader; Gammaprotebacteria rimP leader
+RF01771 Cis-reg; leader; Enterobacteria rnk leader
+RF01772 Cis-reg; leader; Pseudomonas rnk leader
+RF01773 Cis-reg; leader; Pseudomonas rpsL leader
+RF01774 Cis-reg; leader; Rickettsia rpsL leader
+RF01775 Gene; sRNA; RNA S.aureus Orsay G
+RF01776 Gene; antitoxin; RNA anti-toxin A
+RF01779 Gene; AS1726 sRNA
+RF01780 Gene; AS1890 sRNA
+RF01781 Gene; sRNA; ASdes TB sRNA
+RF01782 Gene; antisense; ASpks TB sRNA
+RF01783 Gene; sRNA; Mycobacterium B11
+RF01784 Gene; sRNA; bablM sRNA
+RF01786 Cis-reg; riboswitch; Cyclic di-GMP-II riboswitch
+RF01791 Gene; sRNA; F6 TB sRNA
+RF01793 Gene; sRNA; ffh sRNA
+RF01794 Gene; antitoxin; sok antitoxin (CssrC)
+RF01795 Cis-reg; thermoregulator; FourU thermometer RNA element
+RF01796 Gene; sRNA; Fumarate/nitrate reductase regulator sRNA
+RF01797 Gene; antitoxin; Fst antitoxin sRNA
+RF01798 Gene; G2
+RF01804 Cis-reg; thermoregulator; Lambda phage CIII thermoregulator element
+RF01808 Gene; sRNA; MicX Vibrio cholerae sRNA
+RF01809 Gene; antitoxin; SymR antitoxin
+RF01810 Gene; sRNA; pntA sRNA
+RF01811 Gene; antitoxin; Plasmid transferred anti-sense RNA
+RF01812 Gene; sRNA; Pxr regulatory sRNA
+RF01813 Gene; antitoxin; rdlD antitoxin
+RF01814 Gene; sRNA; rhtB sRNA
+RF01815 Gene; sRNA; rpsB sRNA
+RF01816 Gene; sRNA; RNA Staph. aureus A
+RF01817 Gene; sRNA; RNA Staph. aureus A
+RF01818 Gene; sRNA; RNA Staph. aureus C
+RF01819 Gene; sRNA; RNA Staph. aureus D
+RF01820 Gene; sRNA; RNA Staph. aureus E (RoxS)
+RF01821 Gene; sRNA; RNA Staph. aureus H
+RF01822 Gene; sRNA; RNA Staph. aureus A
+RF01823 Gene; sRNA; rpsL sRNA
+RF01826 Cis-reg; riboswitch; SAM-V riboswitch
+RF01827 Gene; sRNA; SAR11_0636 sRNA
+RF01828 Gene; sRNA; Small pathogenicity island RNA D
+RF01830 Gene; Salmonella enterica Typhi npcRNA 44
+RF01831 Cis-reg; riboswitch; THF riboswitch
+RF01832 Cis-reg; thermoregulator; Repression of heat shock gene expression (ROSE) element
+RF01836 Cis-reg; frameshift_element; ribosomal frameshift site
+RF01842 Cis-reg; frameshift_element; mycoplasma ribosomal frameshift element
+RF01843 Cis-reg; frameshift_element; neiserria ribosomal frameshift element
+RF01846 Gene; snRNA; snoRNA; CD-box; Fungal small nucleolar RNA U3
+RF01854 Gene; Bacterial large signal recognition particle RNA
+RF01855 Gene; Plant signal recognition particle RNA
+RF01856 Gene; Protozoan signal recognition particle RNA
+RF01857 Gene; Archaeal signal recognition particle RNA
+RF01858 Gene; sRNA; RNA Staph. aureus F
+RF01859 Cis-reg; leader; Phenylalanine leader peptide
+RF01867 Gene; sRNA; caulobacter sRNA CC2171
+RF01982 Cis-reg; Pyrrolysine insertion sequence 1
+RF01988 Cis-reg; Selenocysteine insertion sequence 2
+RF01989 Cis-reg; Selenocysteine insertion sequence 3
+RF01990 Cis-reg; Selenocysteine insertion sequence 4
+RF01998 Intron; Group II catalytic intron D1-D4-1
+RF01999 Intron; Group II catalytic intron D1-D4-2
+RF02000 Gene; miRNA; microRNA MIR1846
+RF02001 Intron; Group II catalytic intron D1-D4-3
+RF02003 Intron; Group II catalytic intron D1-D4-4
+RF02004 Intron; Group II catalytic intron D1-D4-5
+RF02005 Intron; Group II catalytic intron D1-D4-6
+RF02012 Intron; Group II catalytic intron D1-D4-7
+RF02029 Gene; sRNA; sraA
+RF02030 Gene; sRNA; tp2
+RF02031 Gene; sRNA; tpke11
+RF02032 Gene; Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA
+RF02033 Gene; HNH endonuclease-associated RNA and ORF (HEARO) RNA
+RF02034 Gene; IMES-1 RNA motif
+RF02035 Gene; IMES-2 RNA motif
+RF02048 Gene; sRNA; Salmonella enterica conserved region STnc30
+RF02049 Gene; sRNA; Salmonella enterica sRNA STnc460
+RF02050 Gene; sRNA; Salmonella enterica sRNA STnc470
+RF02051 Gene; sRNA; Enterobacterial sRNA STnc450
+RF02052 Gene; sRNA; Enterobacterial sRNA STnc630
+RF02053 Gene; sRNA; Enterobacterial sRNA STnc430
+RF02054 Gene; sRNA; Salmonella enterica sRNA STnc420
+RF02055 Gene; sRNA; Enterobacterial sRNA STnc380
+RF02056 Gene; sRNA; Salmonella sRNA STnc390
+RF02057 Gene; sRNA; Salmonella enterica sRNA STnc40
+RF02058 Gene; Gammaproteobacterial sRNA STnc400
+RF02059 Gene; sRNA; Salmonella enterica sRNA STnc40
+RF02060 Gene; sRNA; Enterobacterial sRNA STnc410
+RF02062 Gene; sRNA; Salmonella enterica sRNA STnc361
+RF02063 Gene; sRNA; Salmonella enterica sRNA STnc350
+RF02064 Gene; sRNA; Enterobacterial sRNA STnc370
+RF02065 Gene; sRNA; Enterobacterial sRNA STnc340
+RF02066 Gene; sRNA; Salmonella enterica sRNA STnc320
+RF02067 Gene; sRNA; Salmonella enterica sRNA STnc310
+RF02068 Gene; sRNA; Enterobacterial sRNA STnc480
+RF02069 Gene; sRNA; Enterobacterial sRNA STnc70
+RF02070 Gene; sRNA; Salmonella enterica sRNA STnc300
+RF02071 Gene; sRNA; Salmonella enterica sRNA STnc280
+RF02072 Gene; sRNA; Salmonella enterica sRNA STnc590
+RF02073 Gene; sRNA; Salmonella enterica sRNA STnc260
+RF02074 Gene; sRNA; Enterobacterial sRNA STnc240
+RF02075 Gene; sRNA; Enterobacterial sRNA STnc230
+RF02076 Gene; sRNA; Gammaproteobacterial sRNA STnc100
+RF02077 Gene; sRNA; Salmonella enterica sRNA STnc220
+RF02078 Gene; sRNA; Salmonella enterica sRNA STnc210
+RF02079 Gene; sRNA; Enterobacterial sRNA STnc180
+RF02080 Gene; sRNA; Salmonella enterica sRNA STnc170
+RF02081 Gene; sRNA; Enterobacterial sRNA STnc550
+RF02082 Gene; sRNA; Enterobacterial sRNA STnc540
+RF02083 Gene; antitoxin; OrzO-P RNA antitoxin family
+RF02084 Gene; sRNA; Enterobacteria sRNA STnc130
+RF02088 Gene; sRNA; Enterobacterial sRNA STnc510
+RF02099 Gene; sRNA; rivX sRNA
+RF02100 Gene; sRNA; Translational regulator of tfoXVC
+RF02111 Gene; IS009
+RF02144 Gene; rsmX
+RF02194 Gene; antisense; Bacterial antisense RNA HPnc0260
+RF02221 Gene; sRNA; sRNA-Xcc1
+RF02222 Gene; sRNA; Xanthomonas sRNA sX2
+RF02223 Gene; sRNA; Proteobacterial sRNA sX4
+RF02224 Gene; sRNA; Xanthomonadaceae sRNA sX5
+RF02225 Gene; sRNA; Proteobacterial sRNA sX6
+RF02226 Gene; sRNA; Xanthomonas sRNA sX7
+RF02227 Gene; sRNA; Proteobacterial sRNA sX8
+RF02228 Gene; sRNA; Xanthomonas sRNA sX9
+RF02230 Gene; sRNA; Proteobacterial sRNA sX11
+RF02231 Gene; sRNA; Xanthomonas sRNA sX12
+RF02232 Gene; sRNA; Xanthomonadaceae sRNA sX13
+RF02233 Gene; sRNA; Xanthomonas sRNA sX14/Xoo3
+RF02234 Gene; sRNA; Xanthomonadaceae sRNA sX15
+RF02235 Gene; sRNA; Xanthomonadaceae sRNA asX1
+RF02236 Gene; sRNA; Xanthomonas sRNA asX2
+RF02237 Gene; sRNA; Xanthomonas sRNA asX3
+RF02238 Gene; sRNA; Xanthomonas sRNA asX4/Xoo4
+RF02239 Gene; sRNA; Xanthomonas sRNA asX6
+RF02240 Gene; sRNA; Xanthomonadaceae sRNA Xoo1
+RF02241 Gene; sRNA; Xanthomonadaceae sRNA Xoo2
+RF02242 Gene; sRNA; Xanthomonadaceae sRNA Xoo5
+RF02243 Gene; sRNA; Proteobacterial sRNA Xoo8
+RF02253 Cis-reg; Iron response element II
+RF02268 Gene; sRNA; MtlS RNA
+RF02269 Gene; sRNA; Heliobacter pylori small RNA HPnc0580
+RF02270 Gene; Neisseria sigma-E sRNA
+RF02273 Gene; FsrA
+RF02274 Gene; AniS
+RF02276 Gene; ribozyme; Hammerhead ribozyme (type II)
+RF02278 Gene; sRNA; Betaproteobacteria toxic small RNA
+RF02341 Gene; sRNA; Mycobacterium sRNA ncrMT1302
+RF02342 Gene; sRNA; Alphaproteobacterial sRNA ar7
+RF02343 Gene; sRNA; Alphaproteobacterial sRNA ar9
+RF02344 Gene; sRNA; Alphaproteobacterial ar14
+RF02345 Gene; sRNA; Alphaproteobacterial ar15
+RF02346 Gene; sRNA; Alphaproteobacterial sRNA ar35
+RF02347 Gene; sRNA; Alphaproteobacterial sRNA ar45
+RF02348 Gene; Trans-activating crRNA
+RF02349 Gene; sRNA; Proteobacterial sRNA psRNA2
+RF02350 Gene; sRNA; Nitrosomonas sRNA psRNA6
+RF02351 Gene; sRNA; Proteobacteria sRNA psRNA14
+RF02353 Gene; sRNA; Bradyrhizobiaceae sRNA BjrC68
+RF02354 Gene; sRNA; Bradyrhizobiaceae sRNA BjrC80
+RF02355 Gene; sRNA; Bradyrhizobiaceae sRNA BjrC174
+RF02356 Gene; sRNA; Alphaproteobacterial sRNA BjrC1505
+RF02358 Cis-reg; thermoregulator; Hsp17 thermometer
+RF02360 Gene; sRNA; Cyanobacterial functional RNA 8/9
+RF02362 Gene; sRNA; Cyanobacterial functional RNA 10
+RF02363 Gene; sRNA; Cyanobacterial functional RNA 11
+RF02364 Gene; sRNA; Cyanobacterial functional RNA 13
+RF02365 Gene; sRNA; Cyanobacterial functional RNA 17
+RF02366 Gene; sRNA; Cyanobacterial functional RNA 19
+RF02367 Gene; sRNA; Cyanobacterial functional RNA 20
+RF02368 Gene; sRNA; Cyanobacterial functional RNA 21
+RF02369 Gene; sRNA; h2cR sRNA
+RF02370 Cis-reg; leader; Bacillus tryptophan operon leader
+RF02371 Cis-reg; leader; PyrG leader
+RF02372 Cis-reg; leader; PyrC leader
+RF02373 Cis-reg; leader; PyrD leader
+RF02374 Gene; sRNA; Yersinia YenS sRNA
+RF02375 Gene; sRNA; Aar sRNA
+RF02376 Gene; sRNA; SR1 sRNA
+RF02377 Gene; sRNA; SurA sRNA
+RF02378 Gene; sRNA; SurC sRNA
+RF02379 Gene; sRNA; Cia-dependent small RNA csRNA1
+RF02384 Gene; sRNA; FasX small RNA
+RF02385 Gene; sRNA; Staphylococcus sRNA sau-13
+RF02386 Gene; sRNA; Staphylococcus sRNA sau-19
+RF02387 Gene; sRNA; Staphylococcus sRNA sau-27
+RF02388 Gene; sRNA; Staphylococcus sRNA sau-30
+RF02389 Gene; sRNA; Staphylococcus sRNA sau-31
+RF02390 Gene; sRNA; Staphylococcus sRNA sau-41
+RF02392 Gene; sRNA; Staphylococcus sRNA sau-53
+RF02393 Gene; sRNA; Staphylococcus sRNA sau-59
+RF02394 Gene; sRNA; Staphylococcus sRNA sau-63
+RF02395 Gene; sRNA; Staphylococcus sRNA sau-66
+RF02396 Gene; sRNA; Staphylococcus sRNA sau-5949
+RF02397 Gene; sRNA; Staphylococcus sRNA sau-5971
+RF02398 Gene; sRNA; Staphylococcus sRNA sau-6072
+RF02399 Gene; sRNA; Nitrogen stress-induced RNA 1
+RF02401 Cis-reg; ClpQY promoter
+RF02404 Gene; sRNA; Pseudomonas sRNA P33
+RF02405 Gene; sRNA; Pseudomonas sRNA P34
+RF02414 Gene; sRNA; Listeria sRNA rli60
+RF02415 Gene; sRNA; Listeria sRNA rliG
+RF02417 Gene; sRNA; VR-RNA
+RF02418 Gene; sRNA; Streptococcus sRNA Spd-sr07
+RF02419 Gene; sRNA; Streptococcus sRNA Spd-sr37
+RF02420 Gene; sRNA; Burkholderia sRNA Bp1_Cand612_SIPHT
+RF02421 Gene; sRNA; Burkholderia sRNA Bp1_Cand684_SIPHT
+RF02422 Gene; sRNA; Burkholderia sRNA Bp1_Cand738_SIPHT
+RF02423 Gene; sRNA; Burkholderia sRNA Bp1_Cand871_SIPHT
+RF02424 Gene; sRNA; Burkholderia sRNA Bp2_Cand287_SIPHT
+RF02425 Gene; sRNA; Streptococcus sRNA SpF01
+RF02426 Gene; sRNA; Streptococcus sRNA SpF03
+RF02427 Gene; sRNA; Streptococcus sRNA SpF10
+RF02428 Gene; sRNA; Streptococcus sRNA SpF11
+RF02429 Gene; sRNA; Streptococcus sRNA SpF14
+RF02430 Gene; sRNA; Streptococcus sRNA SpF19
+RF02431 Gene; sRNA; Streptococcus sRNA SpF22
+RF02432 Gene; sRNA; Streptococcus sRNA SpF25
+RF02433 Gene; sRNA; Streptococcus sRNA SpF36
+RF02434 Gene; sRNA; Streptococcus sRNA SpF39
+RF02435 Gene; sRNA; Streptococcus sRNA SpF41
+RF02436 Gene; sRNA; Streptococcus sRNA SpF43
+RF02437 Gene; sRNA; Streptococcus sRNA SpF44
+RF02438 Gene; sRNA; Streptococcus sRNA SpF51
+RF02439 Gene; sRNA; Streptococcus sRNA SpF56
+RF02440 Gene; sRNA; Streptococcus sRNA SpF59 (ldcC RNA)
+RF02441 Gene; sRNA; Streptococcus sRNA SpF61
+RF02442 Gene; sRNA; Streptococcus sRNA SpF66
+RF02443 Gene; sRNA; Streptococcus sRNA SpR08
+RF02444 Gene; sRNA; Streptococcus sRNA SpR10
+RF02445 Gene; sRNA; Streptococcus sRNA SpR14
+RF02446 Gene; sRNA; Streptococcus sRNA SpR18
+RF02447 Gene; sRNA; Streptococcus sRNA SpR19
+RF02448 Gene; sRNA; Streptococcus sRNA SpR20
+RF02449 Gene; sRNA; Bacillus sRNA ncr1015
+RF02450 Gene; sRNA; Bacillus sRNA ncr1175
+RF02451 Gene; sRNA; Bacillus sRNA ncr1241
+RF02452 Gene; sRNA; Bacillus sRNA ncr1575
+RF02453 Gene; sRNA; Bacillus sRNA ncr952
+RF02454 Gene; sRNA; Bacillus sRNA ncr982
+RF02463 Gene; sRNA; Mycobacterium sRNA Ms_AS-1
+RF02464 Gene; sRNA; Actinobacteria sRNA Ms_AS-4
+RF02465 Gene; sRNA; Mycobacterium sRNA Ms_AS-5
+RF02466 Gene; sRNA; Actinobacteria sRNA Ms_AS-8
+RF02467 Gene; sRNA; Mycobacterium sRNA Ms_IGR-2
+RF02468 Gene; sRNA; Mycobacterium sRNA Ms_IGR-4
+RF02469 Gene; sRNA; Actinobacteria sRNA Ms_IGR-7
+RF02470 Gene; sRNA; Mycobacterium sRNA Ms_IGR-8
+RF02471 Gene; sRNA; Actinobacteria sRNA Ms_IGR-5
+RF02495 Gene; antitoxin; Oppression of Hydrophobic ORF by sRNA
+RF02496 Gene; sRNA; Rhizobiales sRNA Atu_At1
+RF02497 Gene; sRNA; Rhizobiales sRNA Atu_C10
+RF02498 Gene; sRNA; Rhizobiales sRNA Atu_C3
+RF02499 Gene; sRNA; Rhizobiales sRNA Atu_C4
+RF02500 Gene; sRNA; EcpR1
+RF02501 Gene; sRNA; Rhizobiales sRNA Atu_C7
+RF02502 Gene; sRNA; Rhizobiales sRNA Atu_C8
+RF02503 Gene; sRNA; Rhizobiales sRNA Atu_C9
+RF02504 Gene; sRNA; Rhizobiales sRNA Atu_L1
+RF02505 Gene; sRNA; Rhizobiales sRNA Atu_L6
+RF02506 Gene; sRNA; Rhizobiales sRNA Atu_Ti1
+RF02507 Gene; sRNA; Rhizobiales sRNA Atu_Ti3
+RF02508 Gene; sRNA; Rhizobiales sRNA Atu_Ti4
+RF02509 Cis-reg; Pyrrolysine insertion sequence mtbB
+RF02510 Cis-reg; Pyrrolysine insertion sequence mttB
+RF02514 Gene; sRNA; 5' ureB small RNA
+RF02515 Gene; sRNA; AfaR small RNA
+RF02519 Gene; antitoxin; ToxI antitoxin
+RF02523 Cis-reg; thermoregulator; Repression of heat shock gene expression (ROSE) element
+RF02524 Gene; sRNA; Streptococcus sRNA sagA
+RF02525 Gene; sRNA; Streptococcus sRNA SSRC30
+RF02526 Gene; sRNA; Streptococcus sRNA SSRC34
+RF02527 Gene; sRNA; Streptococcus sRNA SSRC38
+RF02528 Gene; sRNA; Streptococcus sRNA SSRC41
+RF02529 Gene; sRNA; Streptococcus sRNA SSRC8
+RF02537 Gene; sRNA; Vibrio ToxT activated RNA TarA
+RF02538 Gene; sRNA; Vibrio ToxT activated RNA TarB
+RF02550 Gene; sRNA; RnaG sRNA
+RF02551 Cis-reg; ABC transporter regulator
+RF02552 Gene; sRNA; RcsR1 sRNA
+RF02553 Gene; sRNA; Y RNA-like
+RF02557 Gene; sRNA; Coxiella burnetii sRNA 1
+RF02558 Gene; antisense; Coxiella burnetii sRNA 2
+RF02559 Gene; antisense; Coxiella burnetii sRNA 4
+RF02560 Gene; antisense; Coxiella burnetii sRNA 9
+RF02561 Gene; sRNA; Coxiella burnetii sRNA 12
+RF02562 Gene; sRNA; Coxiella burnetii sRNA 14
+RF02563 Gene; antisense; Coxiella burnetii sRNA 3
+RF02564 Gene; sRNA; Nucleoid-associated noncoding RNA 4 (CssrE)
+RF02565 Gene; sRNA; Y RNA-like
+RF02566 Gene; sRNA; Mycobacterium smegmatis small RNA 1
+RF02567 Gene; sRNA; Vibrio alginolyticus sRNA 907
+RF02568 Gene; sRNA; Escherichia coli small RNA (uptR) gene
+RF02569 Gene; sRNA; IhtA sRNA
+RF02570 Gene; sRNA; Brucella melitensis small RNA 0117
+RF02571 Gene; sRNA; mcr7 sRNA
+RF02572 Cis-reg; Brucella babR 5'UTR
+RF02573 Gene; sRNA; Lactococcus lactis non-coding RNA 147
+RF02574 Gene; sRNA; Rickettsia sRNA 10
+RF02576 Gene; sRNA; tsr1 small RNA
+RF02577 Gene; sRNA; S. aureus tsr24 small RNA
+RF02578 Gene; sRNA; S. aureus tsr25 small RNA
+RF02579 Gene; sRNA; S. aureus tsr26 small RNA
+RF02580 Gene; sRNA; S. aureus tsr31 small RNA
+RF02581 Gene; sRNA; S. aureus tsr32 small RNA
+RF02582 Gene; sRNA; S. aureus tsr33 small RNA
+RF02583 Gene; sRNA; S. aureus Teg23 small RNA
+RF02589 Gene; sRNA; S. pyogenes small RNA 779816
+RF02590 Gene; sRNA; S. pyogenes small RNA 1186876
+RF02591 Gene; sRNA; S. pyogenes small RNA 1786666
+RF02592 Gene; antisense; S. pyogenes antisense RNA 392987
+RF02593 Gene; sRNA; Nitrogen stress-induced RNA 8
+RF02594 Gene; sRNA; Nitrogen stress-induced RNA 9
+RF02596 Gene; sRNA; Cyanobacteria heterocyst sRNA
+RF02597 Cis-reg; thermoregulator; shuA/chuA 5' UTR thermoregulator
+RF02598 Gene; Epstein-Barr virus stable intronic sequence RNA 2
+RF02599 Gene; sRNA; Brucella sRNA CI408
+RF02600 Gene; sRNA; Brucella sRNA CI27
+RF02601 Gene; sRNA; Brucella sRNA CI337
+RF02602 Gene; sRNA; Brucella sRNA CI414
+RF02603 Gene; sRNA; Brucella sRNA CII26
+RF02604 Gene; sRNA; Brucella sRNA CI153
+RF02605 Gene; sRNA; Streptomyces sRNA scr5239
+RF02606 Gene; sRNA; Acinetobacter sRNA 28
+RF02607 Gene; sRNA; Acinetobacter sRNA 25
+RF02608 Gene; sRNA; Acinetobacter sRNA 11
+RF02609 Gene; sRNA; Brucella sRNA 0602
+RF02610 Gene; sRNA; Brucella sRNA 0709
+RF02611 Gene; sRNA; Brucella sRNA 0653
+RF02612 Gene; sRNA; Brucella sRNA 1350
+RF02613 Gene; sRNA; Brucella sRNA 0739
+RF02614 Gene; sRNA; Brucella sRNA 1073
+RF02615 Gene; sRNA; Brucella sRNA 0626
+RF02616 Gene; sRNA; Streptococcus sRNA 8
+RF02617 Gene; sRNA; Streptococcus sRNA 10
+RF02618 Gene; sRNA; Streptococcus sRNA 34
+RF02619 Gene; sRNA; Brucella sRNA 115
+RF02620 Gene; sRNA; Brucella sRNA 119
+RF02621 Gene; sRNA; Brucella sRNA 120
+RF02622 Gene; sRNA; Brucella sRNA 121
+RF02623 Gene; sRNA; Brucella sRNA 140
+RF02624 Gene; sRNA; Brucella sRNA 150
+RF02625 Gene; sRNA; Wolbachia sRNA 46
+RF02626 Gene; sRNA; Wolbachia sRNA 59
+RF02627 Gene; sRNA; Shigella small RNA 1
+RF02628 Gene; sRNA; Hfq-regulated sRNA 1
+RF02629 Gene; sRNA; Regulator of motility and amylovoran A
+RF02630 Gene; sRNA; Hfq-regulated sRNA 12
+RF02631 Gene; sRNA; Hfq-regulated sRNA 13
+RF02632 Gene; sRNA; Hfq-regulated sRNA 10
+RF02633 Gene; sRNA; Hfq-regulated sRNA 21
+RF02634 Gene; sRNA; Enterococcus sRNA EF3314_EF3315
+RF02635 Gene; sRNA; Enterococcus sRNA EF0820_EF0821
+RF02636 Gene; sRNA; Enterococcus sRNA EF1368_EF1369
+RF02637 Gene; sRNA; Enterococcus sRNA EF0408_EF0409
+RF02638 Gene; sRNA; Enterococcus sRNA EF0605_EF0606
+RF02639 Gene; sRNA; Enterococcus sRNA EF0869_EF0870
+RF02640 Gene; sRNA; S. pyogenes small RNA MOSES4
+RF02641 Gene; sRNA; S. pyogenes small RNA Spy490483c
+RF02642 Gene; sRNA; S. pyogenes small RNA Spy491311c
+RF02643 Gene; sRNA; S. pyogenes small RNA Spy491738
+RF02644 Gene; sRNA; S. pyogenes small RNA Spy490380c
+RF02645 Gene; sRNA; Ruegeria cis2 sRNA
+RF02646 Gene; sRNA; Ruegeria cis8 sRNA
+RF02647 Gene; sRNA; Ruegeria cis52 sRNA
+RF02648 Gene; sRNA; Ruegeria cis90 sRNA
+RF02649 Gene; sRNA; Ruegeria trans44 sRNA
+RF02650 Gene; sRNA; Cag non-coding RNA1
+RF02651 Gene; sRNA; Singlet oxygen resistance RNA Y
+RF02652 Gene; sRNA; Salmonella enterica Typhi npcRNA 3
+RF02653 Gene; sRNA; Salmonella enterica Typhi npcRNA 143
+RF02654 Gene; sRNA; MicL sRNA
+RF02655 Gene; sRNA; Brucella BSR0441 sRNA
+RF02659 Gene; sRNA; ncRv12659 sRNA
+RF02660 Cis-reg; icaR 3'UTR
+RF02661 Cis-reg; icaR 5' UTR
+RF02662 Gene; antisense; Bacillus asRNA 0872
+RF02671 Gene; sRNA; Yersinia sRNA 35
+RF02672 Gene; sRNA; Small pathogenicity island RNA X
+RF02673 Gene; sRNA; Streptomyces sRNA 4677
+RF02674 Gene; antisense; antisense RNA of dnaA mRNA
+RF02675 Gene; sRNA; Yersinia sRNA 141
+RF02676 Gene; sRNA; Enterohemorrhagic E. coli sRNA 41
+RF02677 Gene; sRNA; Nitrogen stress-induced RNA 4
+RF02678 Gene; ribozyme; Hatchet ribozyme
+RF02679 Gene; ribozyme; Pistol ribozyme
+RF02680 Cis-reg; riboswitch; PreQ1-III riboswitch
+RF02681 Gene; ribozyme; Twister_sister_ribozyme
+RF02682 Gene; ribozyme; HDV ribozyme from F. prausnitzii
+RF02683 Cis-reg; riboswitch; NiCo riboswitch
+RF02684 Gene; ribozyme; Type-P5 twister ribozyme
+RF02685 Gene; ribozyme; RAGATH-5 RNA
+RF02687 Gene; ribozyme; RAGATH-8 RNA
+RF02688 Gene; ribozyme; RAGATH-13 RNA
+RF02689 Cis-reg; hilD 3'UTR
+RF02690 Gene; sRNA; Burkholderia sRNA 1
+RF02691 Gene; sRNA; Burkholderia sRNA 19
+RF02692 Gene; sRNA; Burkholderia sRNA 39
+RF02693 Gene; sRNA; psm_mec locus RNA
+RF02694 Gene; sRNA; RalR antitoxin
+RF02695 Gene; sRNA; Nitrogen regulated small RNA
+RF02696 Gene; sRNA; Teg49 sRNA
+RF02698 Cis-reg; thermoregulator; Avalong 5' UTR thermometer
+RF02699 Cis-reg; thermoregulator; Avashort 5' UTR thermometer
+RF02700 Cis-reg; thermoregulator; HtrA 5' UTR thermometer
+RF02702 Gene; sRNA; Anti GcvB sRNA
+RF02703 Gene; sRNA; Anti stx2 sRNA
+RF02704 Cis-reg; thermoregulator; LcrF intergenic thermometer
+RF02713 Gene; sRNA; Mycoplasma sRNA MCS4
+RF02728 Gene; sRNA; Haemophilus regulatory RNA responsive to iron
+RF02729 Gene; sRNA; Aggregatibacter sRNA JA01
+RF02730 Gene; sRNA; Aggregatibacter sRNA JA02
+RF02731 Gene; sRNA; Aggregatibacter sRNA JA03
+RF02732 Gene; sRNA; Aggregatibacter sRNA JA04
+RF02733 Cis-reg; thermoregulator; ToxT 5' UTR thermometer
+RF02734 Gene; sRNA; Corynebacterium sRNA 105
+RF02737 Gene; antisense; Soft rot Enterobacteriaceae Rev 13 asRNA
+RF02738 Gene; antisense; Soft rot Enterobacteriaceae Rev 24 asRNA
+RF02739 Gene; sRNA; Soft rot Enterobacteriaceae Rev 41 sRNA
+RF02742 Gene; antisense; Soft rot Enterobacteriaceae Rev 72 asRNA
+RF02743 Gene; antisense; Saccharopolyspora sRNA 389
+RF02744 Cis-reg; Soft rot Enterobacteriaceae Rev 39 5'UTR
+RF02745 Cis-reg; Soft rot Enterobacteriaceae Rev 42 5'UTR
+RF02747 Gene; sRNA; Francisella sRNA A
+RF02748 Gene; sRNA; Francisella sRNA B
+RF02749 Gene; sRNA; Wolbachia sRNA mel02
+RF02750 Gene; sRNA; ES003 sRNA
+RF02751 Gene; sRNA; ES036 (CssrF) sRNA
+RF02752 Gene; sRNA; ES056 sRNA
+RF02753 Gene; sRNA; ES173 sRNA
+RF02754 Gene; sRNA; ES205 sRNA
+RF02755 Gene; sRNA; ES222 sRNA
+RF02756 Gene; sRNA; ES239 sRNA
+RF02757 Gene; sRNA; Erse small RNA
+RF02758 Cis-reg; thermoregulator; RhlA 5' UTR ROSE like thermometer
+RF02759 Cis-reg; thermoregulator; LasI 5' UTR ROSE like thermometer
+RF02760 Gene; sRNA; sR035 sRNA
+RF02761 Gene; sRNA; sR084 sRNA
+RF02762 Cis-reg; thermoregulator; C1_109596F 5' UTR thermometer
+RF02763 Gene; sRNA; IsrM sRNA
+RF02764 Gene; sRNA; Yersinia sRNA 190
+RF02765 Gene; sRNA; Yersinia sRNA 209
+RF02766 Gene; sRNA; Yersinia sRNA 49
+RF02767 Gene; sRNA; Yersinia sRNA 186/sR026/CsrC
+RF02768 Gene; sRNA; Yersinia sRNA 155(RyfD)
+RF02769 Gene; sRNA; Yersinia sRNA 202
+RF02770 Gene; sRNA; Yersinia sRNA 224
+RF02771 Cis-reg; thermoregulator; CnfY 5' UTR thermometer
+RF02772 Cis-reg; thermoregulator; AilA 5' UTR thermometer
+RF02773 Cis-reg; thermoregulator; TrxA 5' UTR thermometer
+RF02774 Cis-reg; thermoregulator; KatA 5' UTR thermometer
+RF02775 Cis-reg; thermoregulator; SodB 5' UTR thermometer
+RF02776 Cis-reg; thermoregulator; SodC 5' UTR thermometer
+RF02777 Cis-reg; thermoregulator; OppA 5' UTR thermometer
+RF02778 Cis-reg; thermoregulator; FdoG-1 5' UTR thermometer
+RF02779 Cis-reg; thermoregulator; PepN 5' UTR thermometer
+RF02780 Cis-reg; thermoregulator; PutA 5' UTR thermometer
+RF02781 Cis-reg; thermoregulator; ManX 5' UTR thermometer
+RF02784 Gene; sRNA; Singlet oxygen resistance RNA X
+RF02790 Gene; sRNA; sodF sRNA
+RF02791 Gene; sRNA; Conserved CCUCCUCCC motif stress-induced RNA 1
+RF02797 Gene; sRNA; Plasmid-encoded Shigella sRNA A
+RF02798 Gene; sRNA; Chromosome-encoded Shigella sRNA A
+RF02799 Gene; sRNA; Chromosome-encoded Shigella sRNA B
+RF02800 Gene; sRNA; Rickettsia sRNA47
+RF02809 Gene; sRNA; RsmW RNA family
+RF02810 Cis-reg; thermoregulator; Lst 5' UTR thermometer
+RF02811 Cis-reg; thermoregulator; FHbp 5' UTR thermometer
+RF02812 Gene; antisense; anti ponA RNA
+RF02813 Cis-reg; thermoregulator; Pseudomonas PA5194 thermometer
+RF02815 Cis-reg; thermoregulator; Lig 5' UTR thermometer
+RF02818 Gene; antisense; Vibrio RNA AS5
+RF02819 Gene; antisense; Vibrio RNA AS7
+RF02820 Gene; antisense; Vibrio RNA AS9
+RF02821 Gene; sRNA; Vibrio RNA IGR5
+RF02822 Gene; sRNA; Streptococcus RNA 266
+RF02823 Gene; sRNA; Legionella RNA 69
+RF02824 Gene; sRNA; Legionella RNA 10
+RF02825 Gene; sRNA; Legionella RNA 17
+RF02826 Gene; sRNA; Streptomyces RNA 6925
+RF02827 Gene; sRNA; Streptomyces RNA 6106
+RF02828 Gene; sRNA; Streptomyces RNA 3920
+RF02829 Gene; sRNA; Streptomyces RNA 4115
+RF02830 Gene; sRNA; Streptomyces RNA 1601
+RF02831 Gene; sRNA; Streptomyces RNA 2736
+RF02832 Gene; sRNA; Streptomyces RNA 5676
+RF02833 Gene; sRNA; Streptomyces RNA 3202
+RF02834 Gene; sRNA; Vibrio RNA VqmR
+RF02835 Gene; sRNA; Burkholderia RNA 11
+RF02836 Gene; sRNA; Burkholderia RNA 14
+RF02837 Gene; sRNA; Burkholderia RNA 7 (anti-hemB)
+RF02838 Gene; sRNA; Enterococcus sRNA 55
+RF02839 Gene; antisense; Enterococcus sRNA 66
+RF02840 Gene; sRNA; Enterococcus sRNA 68 (Lacto-3 RNA)
+RF02841 Gene; sRNA; Enterococcus sRNA 70
+RF02842 Gene; sRNA; Enterococcus sRNA A1
+RF02843 Gene; antisense; Enterococcus sRNA A5
+RF02844 Gene; antisense; Enterococcus sRNA A9
+RF02845 Gene; sRNA; Enterococcus sRNA 1C
+RF02846 Gene; antisense; Enterococcus sRNA 84
+RF02847 Gene; sRNA; Enterococcus sRNA 64
+RF02848 Gene; sRNA; Enterococcus sRNA B11
+RF02849 Gene; sRNA; Yersinia sRNA 197
+RF02850 Gene; antisense; Yersinia sRNA 276
+RF02851 Gene; antisense; Yersinia sRNA 283
+RF02852 Gene; sRNA; Yersinia sRNA 206
+RF02854 Gene; sRNA; Yersinia sRNA 100
+RF02855 Gene; antisense; Yersinia sRNA 251
+RF02856 Gene; sRNA; Leptospira sRNA 30_292
+RF02857 Gene; sRNA; Leptospira sRNA 30_255
+RF02858 Gene; sRNA; Actinobacillus sRNA 08
+RF02859 Gene; sRNA; Actinobacillus sRNA 11
+RF02860 Gene; sRNA; Actinobacillus sRNA 14
+RF02861 Gene; sRNA; Neisseria sRNA 84
+RF02862 Gene; sRNA; Enterococcus sRNA 1300
+RF02863 Gene; sRNA; Enterococcus sRNA 2410
+RF02864 Gene; sRNA; Enterococcus sRNA 30
+RF02865 Gene; sRNA; Burkholderia sRNA 1
+RF02866 Gene; sRNA; Burkholderia sRNA 16 (Bc_KC_sr1)
+RF02867 Gene; sRNA; Burkholderia sRNA 11
+RF02868 Gene; sRNA; Burkholderia sRNA 37
+RF02869 Gene; sRNA; Burkholderia sRNA 25
+RF02870 Gene; sRNA; Burkholderia sRNA 35
+RF02871 Gene; sRNA; Burkholderia sRNA 54
+RF02872 Gene; sRNA; sRNA regulator of biofilms A
+RF02873 Gene; antisense; Antisense to traI
+RF02874 Gene; antisense; Antisense to traG
+RF02875 Gene; antisense; Antisense to pHK01_035
+RF02876 Gene; antisense; Antisense to pHK01_099
+RF02877 Gene; sRNA; Neisseria metabolic switch regulator b (RcoF1/NgncR163)
+RF02878 Gene; sRNA; Mesorhizobail RNA 7
+RF02879 Gene; sRNA; Mesorhizobail RNA 10
+RF02880 Gene; sRNA; Mesorhizobail RNA 15
+RF02881 Gene; sRNA; Mesorhizobail RNA 25
+RF02882 Gene; sRNA; Mesorhizobail RNA 36
+RF02883 Gene; sRNA; Burkholderia sRNA 2
+RF02884 Gene; sRNA; Burkholderia sRNA 7
+RF02885 Cis-reg; riboswitch; SAM-VI riboswitch
+RF02886 Gene; sRNA; Mycobacterium sRNA 6715
+RF02887 Cis-reg; leader; Salmonella mgtC leader RNA
+RF02888 Gene; sRNA; Bacillus sRNA 1
+RF02889 Gene; sRNA; Pseudomonas sRNA 6
+RF02890 Gene; sRNA; Small pathogenicity island RNA C (srn_3610)
+RF02891 Gene; antisense; ArsR-gov region gene B
+RF02892 Gene; antisense; Bacillus SR6 antitoxin
+RF02893 Cis-reg; leader; RpsF leader
+RF02894 Gene; sRNA; Staphylococcus sRNA 35 (srn_0335)
+RF02895 Gene; sRNA; Staphylococcus sRNA 414
+RF02896 Gene; sRNA; Staphylococcus sRNA 774
+RF02897 Gene; sRNA; Staphylococcus sRNA 808
+RF02898 Gene; sRNA; Aggregatibacter sRNA 20
+RF02899 Gene; sRNA; Aggregatibacter sRNA 54
+RF02900 Gene; sRNA; Aggregatibacter sRNA 82
+RF02901 Gene; sRNA; Aggregatibacter sRNA 41
+RF02902 Gene; sRNA; Aggregatibacter sRNA 22
+RF02903 Gene; antisense; Aggregatibacter sRNA 96
+RF02904 Gene; sRNA; Aggregatibacter sRNA 69
+RF02907 Cis-reg; leader; patAB leader
+RF02909 Gene; sRNA; Listeria sRNA rli117
+RF02912 Cis-reg; riboswitch; AAC AAD 5' leader riboswitch
+RF02913 Cis-reg; pemK RNA
+RF02914 Cis-reg; DUF805b RNA
+RF02915 Cis-reg; DUF3800-VI RNA
+RF02916 Cis-reg; atpB RNA
+RF02917 Cis-reg; Burkholderiales-2 RNA
+RF02918 Cis-reg; MDR-NUDIX RNA
+RF02919 Cis-reg; ilvB-OMG RNA
+RF02920 Cis-reg; Fusobacteriales-1 RNA
+RF02921 Gene; sRNA; RT-14 RNA
+RF02922 Cis-reg; RAGATH-32 RNA
+RF02923 Cis-reg; HTH-XRE RNA
+RF02924 Gene; sRNA; skipping-rope RNA
+RF02925 Gene; sRNA; 6A RNA
+RF02926 Gene; sRNA; DUF2693-FD RNA
+RF02927 Gene; sRNA; Actino-ugpB RNA
+RF02928 Gene; sRNA; Actinomyces-1 RNA
+RF02929 Cis-reg; algC RNA
+RF02930 Cis-reg; aspS RNA
+RF02931 Gene; sRNA; Bacilli-1 RNA
+RF02932 Gene; sRNA; Betaproteobacteria-1 RNA
+RF02933 Gene; sRNA; ARRPOF RNA
+RF02934 Gene; sRNA; caiA RNA
+RF02935 Gene; sRNA; che1 RNA
+RF02936 Gene; sRNA; Chloroflexus-1 RNA
+RF02937 Gene; sRNA; Clostridiales-2 RNA
+RF02938 Gene; sRNA; COG2827 RNA
+RF02940 Cis-reg; COG3860 RNA
+RF02942 Gene; sRNA; Clostridiales-3 RNA
+RF02943 Gene; sRNA; Bacteroidales-2 RNA
+RF02944 Gene; sRNA; c4-2 RNA
+RF02945 Gene; sRNA; Corio-PBP RNA
+RF02949 Gene; sRNA; Cupriavidus-1 RNA
+RF02951 Cis-reg; DABA-DC-AT RNA
+RF02952 Gene; sRNA; dfrA-dnaX RNA
+RF02954 Cis-reg; DUF3577 RNA
+RF02955 Gene; sRNA; EGFOA RNA
+RF02956 Gene; sRNA; DUF2693 RNA
+RF02957 Gene; sRNA; EFASI RNA
+RF02958 Gene; sRNA; drum RNA
+RF02959 Cis-reg; DUF3085 RNA
+RF02960 Cis-reg; DUF2800 RNA
+RF02961 Gene; sRNA; DUF3800-II RNA
+RF02962 Gene; sRNA; DUF3800-III RNA
+RF02963 Gene; sRNA; DUF3800-IV RNA
+RF02964 Gene; sRNA; DUF3800-V RNA
+RF02965 Gene; sRNA; CyVA-1 RNA
+RF02966 Gene; sRNA; DUF3268 RNA
+RF02967 Gene; sRNA; DUF3800-VII RNA
+RF02968 Gene; sRNA; DUF3800-IX RNA
+RF02969 Gene; sRNA; DUF3800-I RNA
+RF02971 Gene; sRNA; emrB-Lactobacillus RNA
+RF02972 Cis-reg; engA RNA
+RF02973 Gene; sRNA; Enterococcus-1 RNA
+RF02974 Cis-reg; Fibro-purF RNA
+RF02975 Gene; sRNA; DUF3800-XI RNA
+RF02976 Gene; sRNA; Flavobacterium-1 RNA
+RF02977 Cis-reg; folE RNA
+RF02978 Cis-reg; folP RNA
+RF02981 Cis-reg; FTHFS RNA
+RF02982 Cis-reg; gltS RNA
+RF02983 Gene; sRNA; Fibrobacter-1 RNA
+RF02985 Gene; sRNA; ftsZ-DE RNA
+RF02986 Gene; sRNA; FuFi-1 RNA
+RF02987 Gene; sRNA; GA-cis RNA
+RF02988 Gene; sRNA; GEBRO RNA
+RF02989 Gene; sRNA; gntR-DTE RNA
+RF02990 Gene; sRNA; gut-2 RNA
+RF02992 Cis-reg; hya RNA
+RF02993 Cis-reg; ilvH RNA
+RF02994 Gene; sRNA; IMPDH RNA
+RF02996 Gene; sRNA; int-alpA RNA
+RF02999 Cis-reg; ivy-DE RNA
+RF03000 Gene; sRNA; LOOT RNA
+RF03002 Cis-reg; lysM-Prevotella RNA
+RF03003 Cis-reg; GP20-b RNA
+RF03004 Gene; sRNA; Lacto-phage-1 RNA
+RF03005 Cis-reg; lysM-TM7 RNA
+RF03006 Gene; sRNA; M23 RNA
+RF03007 Gene; sRNA; Mahella-1 RNA
+RF03008 Cis-reg; malK-II RNA
+RF03009 Cis-reg; malK-III RNA
+RF03010 Gene; sRNA; mcrA RNA
+RF03011 Gene; sRNA; Methylophilales-1 RNA
+RF03012 Gene; sRNA; Mu-gpT-DE RNA
+RF03013 Gene; sRNA; nadA RNA
+RF03014 Gene; sRNA; Transposase-1 RNA
+RF03015 Gene; sRNA; Transposase-2 RNA
+RF03016 Gene; sRNA; RT-12 RNA
+RF03017 Gene; sRNA; RT-13 RNA
+RF03018 Gene; sRNA; RT-15 RNA
+RF03019 Gene; sRNA; RT-16 RNA
+RF03020 Gene; sRNA; RT-17 RNA
+RF03021 Gene; sRNA; RT-18 RNA
+RF03022 Gene; sRNA; RT-10 RNA
+RF03023 Gene; sRNA; rpfG RNA
+RF03024 Cis-reg; Rothia-sucC RNA
+RF03025 Gene; sRNA; RT-4 RNA
+RF03026 Gene; sRNA; RT-5 RNA
+RF03027 Gene; sRNA; RT-6 RNA
+RF03028 Gene; sRNA; RT-7 RNA
+RF03029 Gene; sRNA; RT-8 RNA
+RF03030 Gene; sRNA; salivarius-1 RNA
+RF03031 Cis-reg; ssnA RNA
+RF03032 Cis-reg; narK RNA
+RF03033 Cis-reg; NLPC-P60 RNA
+RF03034 Gene; sRNA; nrdJ RNA
+RF03035 Gene; sRNA; nqrA-Marinomonas RNA
+RF03036 Gene; sRNA; osmY RNA
+RF03037 Gene; sRNA; PAGEV RNA
+RF03038 Cis-reg; nhaA-II RNA
+RF03039 Cis-reg; Peptidase-S11 RNA
+RF03040 Cis-reg; PGK RNA
+RF03042 Gene; sRNA; porB RNA
+RF03043 Gene; sRNA; Prevotella-2 RNA
+RF03044 Gene; sRNA; Proteo-phage-1 RNA
+RF03045 Gene; sRNA; proV RNA
+RF03046 Gene; sRNA; Pseudomonadales-1 RNA
+RF03050 Gene; sRNA; RAGATH-25 RNA
+RF03052 Gene; sRNA; RAGATH-28 RNA
+RF03054 Cis-reg; NMT1 RNA
+RF03056 Gene; sRNA; RAGATH-35 RNA
+RF03057 Cis-reg; riboswitch; nhaA-I RNA
+RF03058 Cis-reg; riboswitch; sul1 RNA
+RF03059 Gene; sRNA; raiA-hairpin RNA
+RF03060 Cis-reg; uup RNA
+RF03061 Gene; sRNA; uxuA RNA
+RF03062 Cis-reg; xerDC RNA
+RF03063 Gene; sRNA; Streptomyces-metK RNA
+RF03064 Gene; sRNA; RAGATH-18 RNA
+RF03065 Gene; sRNA; IS605-orfB-I RNA
+RF03066 Gene; sRNA; COG3610-DE RNA
+RF03067 Cis-reg; terC RNA
+RF03068 Gene; sRNA; RT-3 RNA
+RF03069 Cis-reg; malK-I RNA
+RF03070 Gene; sRNA; ssNA-helicase RNA
+RF03071 Cis-reg; riboswitch; DUF1646 RNA
+RF03072 Cis-reg; riboswitch; raiA RNA
+RF03073 Gene; sRNA; RT-19 RNA
+RF03074 Cis-reg; Rhodo-rpoB RNA
+RF03075 Gene; sRNA; DUF3800-VIII RNA
+RF03076 Gene; sRNA; Streptomyces-metH RNA
+RF03077 Gene; sRNA; RT-2 RNA
+RF03078 Cis-reg; chrB-a RNA
+RF03079 Gene; sRNA; MISL RNA
+RF03080 Gene; sRNA; RT-9 RNA
+RF03081 Cis-reg; DUF805 RNA
+RF03082 Gene; sRNA; dinG RNA
+RF03085 Gene; sRNA; abiF RNA
+RF03086 Cis-reg; chrB-b RNA
+RF03087 Gene; sRNA; ROOL RNA
+RF03088 Gene; sRNA; Parabacteroides-1 RNA
+RF03090 Cis-reg; lysM-Actino RNA
+RF03091 Gene; sRNA; Clostridium-PBP RNA
+RF03097 Gene; sRNA; RAGATH-21 RNA
+RF03098 Gene; sRNA; RAGATH-22 RNA
+RF03100 Gene; sRNA; RAGATH-27 RNA
+RF03101 Gene; sRNA; RAGATH-31 RNA
+RF03108 Gene; sRNA; Methylosinus-1 RNA
+RF03109 Cis-reg; Thermales-rpoB RNA
+RF03111 Gene; sRNA; Zeta-pan RNA
+RF03112 Gene; sRNA; Staphylococcus-1 RNA
+RF03113 Gene; sRNA; Poribacteria-1 RNA
+RF03114 Gene; sRNA; RT-1 RNA
+RF03115 Gene; sRNA; KDPG-aldolase RNA
=====================================
db/cm/__build/Rfam_viruses_14.1.txt
=====================================
@@ -0,0 +1,239 @@
+RF00004 Gene; snRNA; splicing; U2 spliceosomal RNA
+RF00008 Gene; ribozyme; Hammerhead ribozyme (type III)
+RF00024 Gene; Vertebrate telomerase RNA
+RF00028 Intron; Group I catalytic intron
+RF00029 Intron; Group II catalytic intron
+RF00032 Cis-reg; Histone 3' UTR stem-loop
+RF00036 Cis-reg; HIV Rev response element
+RF00041 Cis-reg; Enteroviral 3' UTR element
+RF00044 Gene; Bacteriophage pRNA
+RF00048 Cis-reg; Enterovirus cis-acting replication element
+RF00061 Cis-reg; IRES; Hepatitis C virus internal ribosome entry site
+RF00094 Gene; ribozyme; Hepatitis delta virus ribozyme
+RF00102 Gene; VA RNA
+RF00106 Gene; antisense; RNAI
+RF00164 Cis-reg; Coronavirus 3' stem-loop II-like motif (s2m)
+RF00165 Cis-reg; Coronavirus 3' UTR pseudoknot
+RF00170 Gene; Retron msr RNA
+RF00171 Cis-reg; Tombusvirus 5' UTR
+RF00173 Gene; ribozyme; Hairpin ribozyme
+RF00175 Cis-reg; Human immunodeficiency virus type 1 dimerisation initiation site
+RF00176 Cis-reg; Tombusvirus 3' UTR region IV
+RF00182 Cis-reg; Coronavirus packaging signal
+RF00184 Cis-reg; Potato virus X cis-acting regulatory element
+RF00185 Cis-reg; Flavivirus 3' UTR cis-acting replication element (CRE)
+RF00192 Cis-reg; Bovine leukaemia virus RNA packaging signal
+RF00193 Cis-reg; Citrus tristeza virus replication signal
+RF00194 Cis-reg; Rubella virus 3' cis-acting element
+RF00196 Cis-reg; Alfalfa mosaic virus RNA 1 5' UTR stem-loop
+RF00209 Cis-reg; IRES; Pestivirus internal ribosome entry site (IRES)
+RF00210 Cis-reg; IRES; Aphthovirus internal ribosome entry site (IRES)
+RF00214 Cis-reg; Retrovirus direct repeat 1 (dr1)
+RF00215 Cis-reg; Tombus virus defective interfering (DI) RNA region 3
+RF00220 Cis-reg; Human rhinovirus internal cis-acting regulatory element (CRE)
+RF00225 Cis-reg; IRES; Tobamovirus internal ribosome entry site (IRES)
+RF00228 Cis-reg; IRES; Hepatitis A virus internal ribosome entry site (IRES)
+RF00229 Cis-reg; IRES; Picornavirus internal ribosome entry site (IRES)
+RF00233 Cis-reg; Tymovirus/Pomovirus/Furovirus tRNA-like 3' UTR element
+RF00250 Gene; miRNA; Trans-activation response element (TAR)
+RF00252 Cis-reg; Alfalfa mosaic virus coat protein binding (CPB) RNA
+RF00260 Cis-reg; Hepatitis C virus (HCV) cis-acting replication element (CRE)
+RF00262 Gene; antisense; sar RNA
+RF00290 Cis-reg; Bamboo mosaic potexvirus (BaMV) cis-regulatory element
+RF00363 Gene; miRNA; mir-BART1 microRNA precursor family
+RF00364 Gene; miRNA; mir-BART2 microRNA precursor family
+RF00365 Gene; miRNA; mir-BHRF1-1 microRNA precursor family
+RF00366 Gene; miRNA; mir-BHRF1-2 microRNA precursor family
+RF00367 Gene; miRNA; mir-BHRF1-3 microRNA precursor family
+RF00374 Cis-reg; Gammaretrovirus core encapsidation signal
+RF00375 Cis-reg; HIV primer binding site (PBS)
+RF00376 Cis-reg; HIV gag stem loop 3 (GSL3)
+RF00384 Cis-reg; Poxvirus AX element late mRNA cis-regulatory element
+RF00385 Cis-reg; Infectious bronchitis virus D-RNA
+RF00386 Cis-reg; Enterovirus 5' cloverleaf cis-acting replication element
+RF00389 Cis-reg; Bamboo mosaic virus satellite RNA cis-regulatory element
+RF00390 Cis-reg; UPSK RNA
+RF00434 Cis-reg; Luteovirus cap-independent translation element (BTE)
+RF00448 Cis-reg; IRES; Epstein-Barr virus nuclear antigen (EBNA) IRES
+RF00453 Cis-reg; Cardiovirus cis-acting replication element (CRE)
+RF00458 Cis-reg; IRES; Cripavirus internal ribosome entry site (IRES)
+RF00459 Cis-reg; Mason-Pfizer monkey virus packaging signal
+RF00465 Cis-reg; Japanese encephalitis virus (JEV) hairpin structure
+RF00467 Cis-reg; Rous sarcoma virus (RSV) primer binding site (PBS)
+RF00468 Cis-reg; Hepatitis C virus stem-loop VII
+RF00469 Cis-reg; Hepatitis C stem-loop IV
+RF00470 Cis-reg; Togavirus 5' plus strand cis-regulatory element
+RF00480 Cis-reg; frameshift_element; HIV Ribosomal frameshift signal
+RF00481 Cis-reg; Hepatitis C virus 3'X element
+RF00496 Cis-reg; Coronavirus SL-III cis-acting replication element (CRE)
+RF00498 Cis-reg; leader; Equine arteritis virus leader TRS hairpin (LTH)
+RF00499 Cis-reg; Human parechovirus 1 (HPeV1) cis regulatory element (CRE)
+RF00500 Cis-reg; Turnip crinkle virus (TCV) repressor of minus strand synthesis H5
+RF00501 Cis-reg; Rotavirus cis-acting replication element (CRE)
+RF00502 Cis-reg; Turnip crinkle virus (TCV) core promoter hairpin (Pr)
+RF00507 Cis-reg; frameshift_element; Coronavirus frameshifting stimulation element
+RF00510 Cis-reg; Tombusvirus internal replication element (IRE)
+RF00511 Cis-reg; IRES; Kaposi's sarcoma-associated herpesvirus internal ribosome entry site
+RF00524 Cis-reg; R2 RNA element
+RF00525 Cis-reg; Flavivirus DB element
+RF00550 Cis-reg; Hepatitis E virus cis-reactive element
+RF00617 Cis-reg; flavivirus capsid hairpin cHP
+RF00620 Cis-reg; Hepatitis C alternative reading frame stem-loop
+RF00863 Gene; miRNA; microRNA mir-BART17
+RF00864 Gene; miRNA; microRNA mir-BART20
+RF00866 Gene; miRNA; microRNA mir-BART3
+RF00867 Gene; miRNA; microRNA mir-BART5
+RF00868 Gene; miRNA; microRNA mir-BART15
+RF00869 Gene; miRNA; microRNA mir-BART7
+RF00874 Gene; miRNA; microRNA mir-BART12
+RF01009 Gene; miRNA; microRNA mir-M7
+RF01047 Cis-reg; HBV RNA encapsidation signal epsilon
+RF01051 Cis-reg; Cyclic di-GMP-I riboswitch
+RF01072 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01073 Cis-reg; Gag/pol translational readthrough site
+RF01074 Cis-reg; frameshift_element; Putative RNA-dependent RNA polymerase ribosomal frameshift site
+RF01075 Cis-reg; Pseudoknot of tRNA-like structure
+RF01076 Cis-reg; frameshift_element; Polymerase ribosomal frameshift site
+RF01077 Cis-reg; Pseudoknot of tRNA-like structure
+RF01078 Cis-reg; 3'-terminal pseudoknot in PYVV
+RF01079 Cis-reg; frameshift_element; Putative RNA-dependent RNA polymerase ribosomal frameshift site
+RF01080 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01081 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01082 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01083 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01084 Cis-reg; Pseudoknot of tRNA-like structure
+RF01085 Cis-reg; Pseudoknot of tRNA-like structure
+RF01088 Cis-reg; Pseudoknot of tRNA-like structure
+RF01091 Cis-reg; 3'-terminal pseudoknot in SPCSV
+RF01092 Cis-reg; Gag/pol translational readthrough site
+RF01094 Cis-reg; frameshift_element; Polymerase ribosomal frameshift site
+RF01095 Cis-reg; 3'-terminal pseudoknot of CuYV/BPYV
+RF01096 Cis-reg; HepA virus 3'-terminal pseudoknot
+RF01097 Cis-reg; frameshift_element; Gag/pro ribosomal frameshift site
+RF01098 Cis-reg; frameshift_element; Gag/pro ribosomal frameshift site
+RF01099 Cis-reg; Pseudoknot of influenza A virus gene
+RF01100 Cis-reg; 3'-terminal pseudoknot in BYV
+RF01101 Cis-reg; Pseudoknot of tRNA-like structure
+RF01102 Cis-reg; leader; 5'-leader pseudoknot of TEV/CVMV
+RF01103 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01104 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01105 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01106 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01107 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01108 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01109 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01111 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01113 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01114 Cis-reg; Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
+RF01313 Cis-reg; Avian HBV RNA encapsidation signal epsilon
+RF01380 Cis-reg; Human immunodeficiency virus type 1 major splice donor
+RF01381 Cis-reg; HIV-1 stem-loop 3 Psi packaging signal
+RF01382 Cis-reg; HIV-1 stem-loop 4 packaging signal
+RF01386 Gene; sRNA; isrB Hfq binding RNA
+RF01394 Gene; sRNA; isrK Hfq binding RNA
+RF01412 Gene; sRNA; BsrG
+RF01415 Cis-reg; Flavivirus 3'UTR stem loop IV
+RF01417 Cis-reg; Retroviral 3'UTR stability element
+RF01418 Cis-reg; HIV pol-1 stem loop
+RF01453 Cis-reg; 3'TE-DR1 translation enhancer element
+RF01454 Cis-reg; 5'UTR enhancer element
+RF01458 Gene; antisense; Listeria snRNA rli23
+RF01466 Gene; sRNA; Listeria sRNA rli34
+RF01479 Gene; sRNA; Listeria sRNA rli48
+RF01486 Cis-reg; Listeria sRNA rli62
+RF01492 Gene; sRNA; Listeria sRNA rli28
+RF01497 Cis-reg; ALIL pseudoknot
+RF01508 Cis-reg; Barley yellow dwarf virus 5'UTR
+RF01516 Gene; snRNA; snoRNA; CD-box; Human herpesvirus 1 small nucleolar RNA
+RF01668 Gene; sRNA; Pseudomonas sRNA P10
+RF01695 Gene; antisense; C4 antisense RNA
+RF01704 Cis-reg; Downstream peptide RNA
+RF01717 Cis-reg; PhotoRC-II RNA
+RF01739 Cis-reg; riboswitch; Glutamine riboswitch
+RF01745 Cis-reg; manA RNA
+RF01761 Cis-reg; wcaG RNA
+RF01768 Cis-reg; frameshift_element; ribosomal frameshift site
+RF01785 Cis-reg; frameshift_element; ribosomal frameshift site
+RF01789 Gene; sRNA; Epstein-Barr virus EBER1
+RF01790 Cis-reg; frameshift_element; ribosomal frameshift site
+RF01792 Cis-reg; frameshift_element; ribosomal frameshift site
+RF01794 Gene; antitoxin; sok antitoxin (CssrC)
+RF01802 Gene; snRNA; Herpesvirus saimiri U RNA1/RNA2
+RF01804 Cis-reg; thermoregulator; Lambda phage CIII thermoregulator element
+RF01828 Gene; sRNA; Small pathogenicity island RNA D
+RF01833 Cis-reg; frameshift_element; ribosomal frameshift site
+RF01834 Cis-reg; frameshift_element; ribosomal frameshift site
+RF01835 Cis-reg; frameshift_element; ribosomal frameshift site
+RF01836 Cis-reg; frameshift_element; ribosomal frameshift site
+RF01837 Cis-reg; frameshift_element; togavirus ribosomal frameshift element
+RF01838 Cis-reg; frameshift_element; sobemovirus ribosomal frameshift elemental
+RF01839 Cis-reg; frameshift_element; eastern equine encephalitis ribosomal frameshift element
+RF01840 Cis-reg; frameshift_element; ribosomal frameshift element
+RF01841 Cis-reg; frameshift_element; venezuelan equine encephalitis virus ribosomal frameshift element
+RF01940 Gene; miRNA; microRNA hvt-mir-H9
+RF02004 Intron; Group II catalytic intron D1-D4-5
+RF02012 Intron; Group II catalytic intron D1-D4-7
+RF02032 Gene; Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA
+RF02033 Gene; HNH endonuclease-associated RNA and ORF (HEARO) RNA
+RF02076 Gene; sRNA; Gammaproteobacterial sRNA STnc100
+RF02111 Gene; IS009
+RF02221 Gene; sRNA; sRNA-Xcc1
+RF02276 Gene; ribozyme; Hammerhead ribozyme (type II)
+RF02340 Cis-reg; Dengue virus SLA
+RF02359 Cis-reg; Bacteriophage MS2 operator hairpin
+RF02415 Gene; sRNA; Listeria sRNA rliG
+RF02416 Cis-reg; Turnip crinkle virus 3'UTR
+RF02435 Gene; sRNA; Streptococcus sRNA SpF41
+RF02455 Cis-reg; Dianthovirus RNA2 cap-independent translation element
+RF02456 Cis-reg; Dianthovirus RNA2 3'UTR stem loops
+RF02457 Cis-reg; Tombusvirus 3' cap-independent translation element
+RF02458 Cis-reg; Aureusvirus cap-independent translation element
+RF02459 Cis-reg; Necrovirus cap-independent translation element
+RF02460 Cis-reg; Satellite tobacco necrosis virus cap-independent translation element
+RF02461 Cis-reg; Blackcurrant reversion virus cap-independent translation element
+RF02521 Cis-reg; Pea enation mosaic virus-2 cap-independent translation element
+RF02522 Cis-reg; Pea enation mosaic virus-2 cap-independent translation element
+RF02532 Cis-reg; Murine norovirus 3'UTR
+RF02533 Cis-reg; Hepatitis A virus (HAV) cis-acting replication element (CRE)
+RF02534 Cis-reg; Norovirus cis-acting replication element (CRE)
+RF02536 Cis-reg; Avian encephalitis virus (AEV) cis-acting replication element (CRE)
+RF02549 Cis-reg; Pseudoknot PSK3
+RF02577 Gene; sRNA; S. aureus tsr24 small RNA
+RF02585 Cis-reg; Hepatitis C virus RNA packaging signal
+RF02586 Cis-reg; Hepatitis C virus RNA packaging signal 733
+RF02587 Cis-reg; Hepatitis C virus RNA packaging signal 4629
+RF02588 Cis-reg; Hepatitis C virus RNA packaging signal 6067
+RF02589 Gene; sRNA; S. pyogenes small RNA 779816
+RF02595 Gene; Epstein-Barr virus stable intronic sequence RNA 1
+RF02598 Gene; Epstein-Barr virus stable intronic sequence RNA 2
+RF02626 Gene; sRNA; Wolbachia sRNA 59
+RF02658 Cis-reg; IRES; Rhopalosiphum padi virus 5'UTR internal ribosome entry site
+RF02672 Gene; sRNA; Small pathogenicity island RNA X
+RF02679 Gene; ribozyme; Pistol ribozyme
+RF02702 Gene; sRNA; Anti GcvB sRNA
+RF02703 Gene; sRNA; Anti stx2 sRNA
+RF02712 Gene; sRNA; Epstein-Barr virus EBER2
+RF02743 Gene; antisense; Saccharopolyspora sRNA 389
+RF02816 Cis-reg; Hepatitis B virus post-transcriptional regulatory element 1151-1410
+RF02838 Gene; sRNA; Enterococcus sRNA 55
+RF02848 Gene; sRNA; Enterococcus sRNA B11
+RF02855 Gene; antisense; Yersinia sRNA 251
+RF02892 Gene; antisense; Bacillus SR6 antitoxin
+RF02897 Gene; sRNA; Staphylococcus sRNA 808
+RF02900 Gene; sRNA; Aggregatibacter sRNA 82
+RF02910 Cis-reg; Coronavirus 5' stem-loops 1-2
+RF02911 Cis-reg; Baculoviridae Nucleocapsid Assembly essential Element
+RF02921 Gene; sRNA; RT-14 RNA
+RF02924 Gene; sRNA; skipping-rope RNA
+RF02931 Gene; sRNA; Bacilli-1 RNA
+RF02944 Gene; sRNA; c4-2 RNA
+RF02996 Gene; sRNA; int-alpA RNA
+RF03003 Cis-reg; GP20-b RNA
+RF03010 Gene; sRNA; mcrA RNA
+RF03021 Gene; sRNA; RT-18 RNA
+RF03022 Gene; sRNA; RT-10 RNA
+RF03044 Gene; sRNA; Proteo-phage-1 RNA
+RF03064 Gene; sRNA; RAGATH-18 RNA
+RF03075 Gene; sRNA; DUF3800-VIII RNA
+RF03085 Gene; sRNA; abiF RNA
+RF03087 Gene; sRNA; ROOL RNA
=====================================
db/cm/__build/archaea.sql
=====================================
@@ -0,0 +1,21 @@
+SELECT DISTINCT f.rfam_acc, f.type, f.description
+FROM taxonomy tx
+INNER JOIN rfamseq rf ON rf.ncbi_id = tx.ncbi_id
+INNER JOIN full_region fr ON fr.rfamseq_acc = rf.rfamseq_acc
+INNER JOIN family f ON f.rfam_acc = fr.rfam_acc
+WHERE ((f.type LIKE 'Gene;' AND f.description NOT LIKE '%transfer-messenger RNA')
+OR f.type LIKE '%CRISPR;'
+OR f.type LIKE '%antisense;'
+OR f.type LIKE '%antitoxin;'
+OR f.type LIKE '%miRNA;'
+OR f.type LIKE '%ribozyme;'
+OR f.type LIKE '%sRNA;'
+OR f.type LIKE '%snRNA%'
+OR f.type LIKE 'Intron;'
+OR f.type LIKE 'Cis-reg;'
+OR f.type LIKE '%IRES;'
+OR f.type LIKE '%frameshift_element;'
+OR f.type LIKE '%leader;'
+OR f.type LIKE '%riboswitch;'
+OR f.type LIKE '%thermoregulator;')
+AND tx.tax_string LIKE 'Archaea%';
=====================================
db/cm/__build/bacteria.sql
=====================================
@@ -0,0 +1,21 @@
+SELECT DISTINCT f.rfam_acc, f.type, f.description
+FROM taxonomy tx
+INNER JOIN rfamseq rf ON rf.ncbi_id = tx.ncbi_id
+INNER JOIN full_region fr ON fr.rfamseq_acc = rf.rfamseq_acc
+INNER JOIN family f ON f.rfam_acc = fr.rfam_acc
+WHERE ((f.type LIKE 'Gene;' AND f.description NOT LIKE '%transfer-messenger RNA')
+OR f.type LIKE '%CRISPR;'
+OR f.type LIKE '%antisense;'
+OR f.type LIKE '%antitoxin;'
+OR f.type LIKE '%miRNA;'
+OR f.type LIKE '%ribozyme;'
+OR f.type LIKE '%sRNA;'
+OR f.type LIKE '%snRNA%'
+OR f.type LIKE 'Intron;'
+OR f.type LIKE 'Cis-reg;'
+OR f.type LIKE '%IRES;'
+OR f.type LIKE '%frameshift_element;'
+OR f.type LIKE '%leader;'
+OR f.type LIKE '%riboswitch;'
+OR f.type LIKE '%thermoregulator;')
+AND tx.tax_string LIKE 'Bacteria%';
=====================================
db/cm/__build/update.sh
=====================================
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+# Inspired by https://github.com/tseemann/prokka/issues/243#issuecomment-341672420
+
+rfamversion=14.1
+
+if [ ! -f Rfam.cm ]; then
+ wget ftp://ftp.ebi.ac.uk/pub/databases/Rfam/${rfamversion}/Rfam.cm.gz
+ gunzip Rfam.cm.gz
+fi
+
+for tax in archaea bacteria viruses; do
+ mysql --user rfamro --host mysql-rfam-public.ebi.ac.uk --port 4497 --database Rfam \
+ < ${tax}.sql \
+ | tail -n +2 \
+ > Rfam_${tax}_${rfamversion}.txt
+ cmfetch -o Rfam_${tax}.cm -f Rfam.cm Rfam_${tax}_${rfamversion}.txt
+ cmconvert -o ${tax} -b Rfam_${tax}.cm
+done
+
+mv archaea ../Archaea
+mv bacteria ../Bacteria
+mv viruses ../Viruses
=====================================
db/cm/__build/viruses.sql
=====================================
@@ -0,0 +1,21 @@
+SELECT DISTINCT f.rfam_acc, f.type, f.description
+FROM taxonomy tx
+INNER JOIN rfamseq rf ON rf.ncbi_id = tx.ncbi_id
+INNER JOIN full_region fr ON fr.rfamseq_acc = rf.rfamseq_acc
+INNER JOIN family f ON f.rfam_acc = fr.rfam_acc
+WHERE ((f.type LIKE 'Gene;' AND f.description NOT LIKE '%transfer-messenger RNA')
+OR f.type LIKE '%CRISPR;'
+OR f.type LIKE '%antisense;'
+OR f.type LIKE '%antitoxin;'
+OR f.type LIKE '%miRNA;'
+OR f.type LIKE '%ribozyme;'
+OR f.type LIKE '%sRNA;'
+OR f.type LIKE '%snRNA%'
+OR f.type LIKE 'Intron;'
+OR f.type LIKE 'Cis-reg;'
+OR f.type LIKE '%IRES;'
+OR f.type LIKE '%frameshift_element;'
+OR f.type LIKE '%leader;'
+OR f.type LIKE '%riboswitch;'
+OR f.type LIKE '%thermoregulator;')
+AND tx.tax_string LIKE 'Viruses%';
=====================================
doc/prokka-manual.txt deleted
=====================================
@@ -1,607 +0,0 @@
-Prokka: rapid prokaryotic genome annotation
-===========================================
-
-Torsten Seemann (torsten.seemann at gmail.com) (@torstenseemann)
-
-Contents
---------
-
-- Introduction
-- Installation
-- Invoking Prokka
-- Output Files
-- Command line options
-- Databases
-- FAQ
-- Changes
-- Citation
-- Dependencies
-
-Introduction
-------------
-
-Whole genome annotation is the process of identifying features of
-interest in a set of genomic DNA sequences, and labelling them with
-useful information. Prokka is a software tool to annotate bacterial,
-archaeal and viral genomes quickly and produce standards-compliant
-output files.
-
-Installation
-------------
-
-Before the main install can begin you need to install some system
-packages:
-
-Centos/Fedora/RHEL (RPM)
-
-``` {.bash}
-sudo yum install perl-Time-Piece perl-XML-Simple perl-Digest-MD5 git java perl-CPAN perl-Module-Build
-sudo cpan -i Bio::Perl # if you don't have Bioperl installed (it will be tedious)
-```
-
-Ubuntu/Debian/Mint (APT)
-
-``` {.bash}
-sudo apt-get install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl
-```
-
-Mac OS X
-
-``` {.bash}
-sudo cpan Time::Piece XML::Simple Digest::MD5 Bio::Perl
-```
-
-There are currently 3 ways to install the main Prokka software: Github,
-Tarball or Homebrew.
-
-Github
-
-Choose somewhere to put it, for example in your home directory (no root
-access required):
-
-``` {.bash}
-% cd $HOME
-```
-
-Clone the latest version of the repository:
-
-``` {.bash}
-% git clone https://github.com/tseemann/prokka.git
-% ls prokka
-```
-
-Index the sequence databases
-
-``` {.bash}
-% prokka/bin/prokka --setupdb
-```
-
-Homebrew
-
-Homebrew is a package manager which allows users to easily install
-complex software in their home directory. Instructions for installing it
-are available for Linux and Mac OS X.
-
-Ensure you have brew installed:
-
-``` {.bash}
-% brew
-```
-
-Make sure you have the homebrew-science tap/channel enabled:
-
-``` {.bash}
-% brew tap homebrew/science
-% brew update
-```
-
-Install Prokka and all its dependencies:
-
-``` {.bash}
-% brew install prokka --HEAD
-```
-
-Tarball
-
-WARNING: this method gives you very old version of prokka. The brew or
-github methods are preferred!
-
-Download the latest prokka-1.xx.tar.gz archive from
-http://www.bioinformatics.net.au/software.prokka.shtml
-
-``` {.bash}
-% wget http://www.vicbioinformatics.com/prokka-1.11.tar.gz
-```
-
-Choose somewhere to put it, for example in your home directory (no root
-access required):
-
-``` {.bash}
-% cd $HOME
-% tar zxvf prokka-1.11.tar.gz
-% ls prokka-1.11
-```
-
-Install dependencies
-
-Prokka comes with many binaries for Linux and Mac OS X. It will always
-use your existing installed versions if they exist, but will use the
-included ones if that fails. For some older systems (eg. Centos 4.x)
-some of them won't work due to them being dynamically linked against new
-GLIBC libraries you don't have. You can consult the list of dependencies
-later in this document.
-
-Choose a rRNA predictor
-
-Option 1 - Don't use one
-
-If Prokka can't find a predictor for rRNA featues (either Barrnap or
-RNAmmer below) then it simply won't annotate any. Most people don't care
-that much about them anyway,
-
-Option 2 - Barrnap
-
-This was written by the author of Prokka and is recommended if you
-prefer speed over absolute accuracy. It uses the new multi-core NHMMER
-for DNA:DNA profile searches. Download it from
-https://github.com/tseemann/barrnap
-
-Option 3 - RNAmmer
-
-RNAmmer was written when HMMER 2.x was the latest release. Since them,
-HMMER 3.x has been released, and uses the same executable binary names.
-Prokka needs HMMER3 and RNAmmer (and hence HMMER2) so you need to edit
-your RNAmmer script to explicitly point your HMMER2 binary instead of
-using the HMMER3 binary which is more likely to be in your PATH first.
-
-Type which rnammer to find the script, and then edit it with your
-favourite editor. Find the following lines at the top:
-
-``` {.perl}
-if ( $uname eq "Linux" ) {
-# $HMMSEARCH_BINARY = "/usr/cbs/bio/bin/linux64/hmmsearch"; # OLD
- $HMMSEARCH_BINARY = "/path/to/my/hmmer-2.3.2/bin/hmmsearch"; # NEW (yours)
-}
-```
-
-If you are using Mac OS X, you'll also have to change the "Linux" to
-"Darwin" too. As you can see, I have commented out the original part,
-and replaced it with the location of my HMMER2 hmmsearch tool, so it
-doesn't run the HMMER3 one. You need to ensure HMMER3 is in your PATH
-before the old HMMER2 too.
-
-Add to PATH
-
-Add the following line to your $HOME/.bashrc file, or to
-/etc/profile.d/prokka.sh to make it available to all users:
-
-``` {.bash}
-export PATH=$PATH:$HOME/prokka-1.11/bin
-```
-
-Index the sequence databases
-
-``` {.bash}
-% prokka --setupdb
-```
-
-Test
-
-- Type prokka and it should output it's help screen.
-- Type prokka --version and you should see an output like prokka 1.x
-- Type prokka --listdb and it will show you what databases it has
- installed to use.
-
-Invoking Prokka
----------------
-
-Beginner
-
-``` {.bash}
-# Vanilla (but with free toppings)
-% prokka contigs.fa
-
-# Look for a folder called PROKKA_yyyymmdd (today's date) and look at stats
-% cat PROKKA_yyyymmdd/*.txt
-```
-
-Moderate
-
-``` {.bash}
-# Choose the names of the output files
-% prokka --outdir mydir --prefix mygenome contigs.fa
-
-# Visualize it in Artemis
-% art mydir/mygenome.gff
-```
-
-Expert
-
-``` {.bash}
-# It's not just for bacteria, people
-% prokka --kingdom Archaea --outdir mydir --genus Pyrococcus --locustag PYCC
-
-# Search for my favourite gene
-% exonerate --bestn 1 zetatoxin.fasta mydir/PYCC_06072012.faa | less
-```
-
-Wizard
-
-``` {.bash}
-# Watch and learn
-% prokka --outdir mydir --locustag EHEC --proteins NewToxins.faa --evalue 0.001 --gram neg --addgenes contigs.fa
-
-# Check to see if anything went really wrong
-% less mydir/EHEC_06072012.err
-
-# Add final details using Sequin
-% sequin mydir/EHEC_0607201.sqn
-```
-
-NCBI Genbank submitter
-
-``` {.bash}
-# Register your BioProject (e.g. PRJNA123456) and your locus_tag prefix (e.g. EHEC) first!
-% prokka --compliant --centre UoN --outdir PRJNA123456 --locustag EHEC --prefix EHEC-Chr1 contigs.fa
-
-# Check to see if anything went really wrong
-% less PRJNA123456/EHEC-Chr1.err
-
-# Add final details using Sequin
-% sequin PRJNA123456/EHEC-Chr1.sqn
-```
-
-European Nucleotide Archive (ENA) submitter
-
-``` {.bash}
-# Register your BioProject (e.g. PRJEB12345) and your locus_tag (e.g. EHEC) prefix first!
-% prokka --compliant --centre UoN --outdir PRJEB12345 --locustag EHEC --prefix EHEC-Chr1 contigs.fa
-
-# Check to see if anything went really wrong
-% less PRJNA123456/EHEC-Chr1.err
-
-# Install and run Sanger Pathogen group's Prokka GFF3 to EMBL converter
-# available from https://github.com/sanger-pathogens/gff3toembl
-# Find the closest NCBI taxonomy id (e.g. 562 for Escherichia coli)
-% gff3_to_embl -i "Submitter, A." \
- -m "Escherichia coli EHEC annotated using Prokka." \
- -g linear -c PROK -n 11 -f PRJEB12345/EHEC-Chr1.embl \
- "Escherichia coli" 562 PRJEB12345 "Escherichia coli strain EHEC" PRJEB12345/EHEC-Chr1.gff
-
-# Download and run the EMBL validator prior to submitting the EMBL flat file
-% curl -L -O ftp://ftp.ebi.ac.uk/pub/databases/ena/lib/embl-client.jar
-% java -jar embl-client.jar -r PRJEB12345/EHEC-Chr1.embl
-
-# Compress the file ready to upload to ENA, and calculate MD5 checksum
-% gzip PRJEB12345/EHEC-Chr1.embl
-% md5sum PRJEB12345/EHEC-Chr1.embl.gz
-```
-
-Crazy Person
-
-``` {.bash}
-# No stinking Perl script is going to control me
-% prokka \
- --outdir $HOME/genomes/Ec_POO247 --force \
- --prefix Ec_POO247 --addgenes --locustag ECPOOp \
- --increment 10 --gffver 2 --centre CDC --compliant \
- --genus Escherichia --species coli --strain POO247 --plasmid pECPOO247 \
- --kingdom Bacteria --gcode 11 --usegenus \
- --proteins /opt/prokka/db/trusted/Ecocyc-17.6 \
- --evalue 1e-9 --rfam \
- plasmid-closed.fna
-```
-
-Output Files
-------------
-
- Extension Description
- ----------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
- .gff This is the master annotation in GFF3 format, containing both sequences and annotations. It can be viewed directly in Artemis or IGV.
- .gbk This is a standard Genbank file derived from the master .gff. If the input to prokka was a multi-FASTA, then this will be a multi-Genbank, with one record for each sequence.
- .fna Nucleotide FASTA file of the input contig sequences.
- .faa Protein FASTA file of the translated CDS sequences.
- .ffn Nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA)
- .sqn An ASN1 format "Sequin" file for submission to Genbank. It needs to be edited to set the correct taxonomy, authors, related publication etc.
- .fsa Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines.
- .tbl Feature Table file, used by "tbl2asn" to create the .sqn file.
- .err Unacceptable annotations - the NCBI discrepancy report.
- .log Contains all the output that Prokka produced during its run. This is a record of what settings you used, even if the --quiet option was enabled.
- .txt Statistics relating to the annotated features found.
- .tsv Tab-separated file of all features: locus_tag,ftype,gene,EC_number,product
-
-Command line options
---------------------
-
- General:
- --help This help
- --version Print version and exit
- --docs Show full manual/documentation
- --citation Print citation for referencing Prokka
- --quiet No screen output (default OFF)
- --debug Debug mode: keep all temporary files (default OFF)
- Setup:
- --listdb List all configured databases
- --setupdb Index all installed databases
- --cleandb Remove all database indices
- --depends List all software dependencies
- Outputs:
- --outdir [X] Output folder [auto] (default '')
- --force Force overwriting existing output folder (default OFF)
- --prefix [X] Filename output prefix [auto] (default '')
- --addgenes Add 'gene' features for each 'CDS' feature (default OFF)
- --locustag [X] Locus tag prefix (default 'PROKKA')
- --increment [N] Locus tag counter increment (default '1')
- --gffver [N] GFF version (default '3')
- --compliant Force Genbank/ENA/DDJB compliance: --genes --mincontiglen 200 --centre XXX (default OFF)
- --centre [X] Sequencing centre ID. (default '')
- Organism details:
- --genus [X] Genus name (default 'Genus')
- --species [X] Species name (default 'species')
- --strain [X] Strain name (default 'strain')
- --plasmid [X] Plasmid name or identifier (default '')
- Annotations:
- --kingdom [X] Annotation mode: Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria')
- --gcode [N] Genetic code / Translation table (set if --kingdom is set) (default '0')
- --gram [X] Gram: -/neg +/pos (default '')
- --usegenus Use genus-specific BLAST databases (needs --genus) (default OFF)
- --proteins [X] Fasta file of trusted proteins to first annotate from (default '')
- --hmms [X] Trusted HMM to first annotate from (default '')
- --metagenome Improve gene predictions for highly fragmented genomes (default OFF)
- --rawproduct Do not clean up /product annotation (default OFF)
- Computation:
- --fast Fast mode - skip CDS /product searching (default OFF)
- --cpus [N] Number of CPUs to use [0=all] (default '8')
- --mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1')
- --evalue [n.n] Similarity e-value cut-off (default '1e-06')
- --rfam Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0')
- --norrna Don't run rRNA search (default OFF)
- --notrna Don't run tRNA search (default OFF)
- --rnammer Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)
-
-Option: --rawproduct
-
-Prokka annotates proteins by using sequence similarity to other proteins
-in its database, or the databses the user provides via --proteins. By
-default, Prokka tries to "cleans" the /product names to ensure they are
-compliant with Genbank/ENA conventions. Some of the main things it does
-is:
-
-- set vague names to hypothetical protein
-- consistifies terms like possible, probable, predicted, ... to
- putative
-- removes EC, COG and locus_tag identifiers
-
-Full details can be found in the cleanup_product() function in the
-prokka script. If you feel your annotations are being ruined, try using
-the --rawproduct option, and please file an issue if you find an example
-of where it is "behaving badly" and I will fix it.
-
-Databases
----------
-
-The Core (BLAST+) Databases
-
-Prokka uses a variety of databases when trying to assign function to the
-predicted CDS features. It takes a hierarchial approach to make it
-fast.
-A small, core set of well characterized proteins are first searched
-using BLAST+. This combination of small database and fast search
-typically completes about 70% of the workload. Then a series of slower
-but more sensitive HMM databases are searched using HMMER3.
-
-The initial core databases are derived from UniProtKB; there is one per
-"kingdom" supported. To qualify for inclusion, a protein must be (1)
-from Bacteria (or Archaea or Viruses); (2) not be "Fragment" entries;
-and (3) have an evidence level ("PE") of 2 or lower, which corresponds
-to experimental mRNA or proteomics evidence.
-
-Making a Core Databases
-
-If you want to modify these core databases, the included script
-prokka-uniprot_to_fasta_db, along with the official uniprot_sprot.dat,
-can be used to generate a new database to put in
-/opt/prokka/db/kingdom/. If you add new ones, the command
-prokka --listdb will show you whether it has been detected properly.
-
-The Genus Databases
-
-If you enable --usegenus and also provide a Genus via --genus then it
-will first use a BLAST database which is Genus specific. Prokka comes
-with a set of databases for the most common Bacterial genera; type
-prokka --listdb to see what they are.
-
-Adding a Genus Databases
-
-If you have a set of Genbank files and want to create a new Genus
-database, Prokka comes with a tool called prokka-genbank_to_fasta_db to
-help. For example, if you had four annotated "Coccus" genomes, you could
-do the following:
-
- % prokka-genbank_to_fasta_db Coccus1.gbk Coccus2.gbk Coccus3.gbk Coccus4.gbk > Coccus.faa
- % cd-hit -i Coccus.faa -o Coccus -T 0 -M 0 -g 1 -s 0.8 -c 0.9
- % rm -fv Coccus.faa Coccus.bak.clstr Coccus.clstr
- % makeblastdb -dbtype prot -in Coccus
- % mv Coccus.p* /path/to/prokka/db/genus/
-
-The HMM Databases
-
-Prokka comes with a bunch of HMM libraries for HMMER3. They are mostly
-Bacteria-specific. They are searched after the core and genus databases.
-You can add more simply by putting them in /opt/prokka/db/hmm. Type
-prokka --listdb to confirm they are recognised.
-
-FASTA database format
-
-Prokka understands two annotation tag formats, a plain one and a
-detailed one.
-
-The plain one is a standard FASTA-like line with the ID after the >
-sign, and the protein /product after the ID (the "description" part of
-the line):
-
- >SeqID product
-
-The detailed one consists of a special encoded three-part description
-line. The parts are the /EC_number, the /gene code, then the /product -
-and they are separated by a special "~" sequence:
-
- >SeqID EC_number~~~gene~~~product
-
-Here are some examples. Note that not all parts need to be present, but
-the "~" should still be there:
-
- >YP_492693.1 2.1.1.48~~~ermC~~~rRNA adenine N-6-methyltransferase
- MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEI
- DHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVF*
- >YP_492697.1 ~~~traB~~~transfer complex protein TraB
- MIKKFSLTTVYVAFLSIVLSNITLGAENPGPKIEQGLQQVQTFLTGLIVAVGICAGVWIV
- LKKLPGIDDPMVKNEMFRGVGMVLAGVAVGAALVWLVPWVYNLFQ*
- >YP_492694.1 ~~~~~~transposase
- MNYFRYKQFNKDVITVAVGYYLRYALSYRDISEILRGRGVNVHHSTVYRWVQEYAPILYQ
- QSINTAKNTLKGIECIYALYKKNRRSLQIYGFSPCHEISIMLAS*
-
-The same description lines apply to HMM models, except the "NAME" and
-"DESC" fields are used:
-
- NAME PRK00001
- ACC PRK00001
- DESC 2.1.1.48~~~ermC~~~rRNA adenine N-6-methyltransferase
- LENG 284
-
-FAQ
----
-
-- Where does the name "Prokka" come from?
- Prokka is a contraction of "prokaryotic annotation". It's also
- relatively unique within Google, and also rhymes with a native
- Australian marsupial called the quokka.
-
-- Can I annotate by eukaryote genome with Prokka?
- No. Prokka is specifically designed for Bacteria, Archaea and
- Viruses. It can't handle multi-exon gene models; I would recommend
- using MAKER 2 for that purpose.
-
-- Why does Prokka keeps on crashing when it gets to tge "tbl2asn"
- stage?
- It seems that the tbl2asn program from NCBI "expires" after 12
- months, and refuses to run. Unfortunately you need to install a
- newer version which you can download from here.
-
-- The hmmscan step seems to hang and do nothing?
- The problem here is GNU Parallel. It seems the Debian package for
- hmmer has modified it to require the --gnu option to behave in the
- 'default' way. There is no clear reason for this. The only way to
- restore normal behaviour is to edit the prokka script and change
- parallel to parallel --gnu.
-
-- Why does prokka fail when it gets to hmmscan?
- Unfortunately HMMER keeps changing it's database format, and they
- aren't upward compatible. If you upgraded HMMER (from 3.0 to 3.1
- say) then you need to "re-press" the files. This can be done as
- follows: cd /path/to/prokka/db/hmm mkdir new for D in .hmm ; do
- hmmconvert D > new/D ; done cd new for D in .hmm ; do hmmpress $D ;
- done mv * .. rmdir new
-
-- Why does Prokka take so long to download?
- Our server is in Australia, and the international pipes aren't
- always flowing as well as we'd like. I try to put it on GoogleDrive.
- Dropbox is no longer possible due to bandwidth quotas. If you are
- able to mirror Prokka (~2 GB) outside please let me know.
-
-- Why can't I load Prokka .GBK files into Mauve?
- Mauve uses BioJava to parse GenBank files, and it is very picky
- about Genbank files. It does not like long contig names, like those
- from Velvet or Spades. One solution is to use --centre XXX in Prokka
- and it will rename all your contigs to be NCBI (and Mauve)
- compliant. It does not like the ACCESSION and VERSION strings that
- Prokka produces via the "tbl2asn" tool. The following Unix command
- will fix them:
- egrep -v '^(ACCESSION|VERSION)' prokka.gbk > mauve.gbk
-
-Bugs
-----
-
-- Submit problems or requests here:
- https://github.com/tseemann/prokka/issues
-
-Changes
--------
-
-- ChangeLog.txt:
- https://raw.githubusercontent.com/tseemann/prokka/master/doc/ChangeLog.txt
-- Github commits: https://github.com/tseemann/prokka/commits/master
-
-Citation
---------
-
-Seemann T.
-Prokka: rapid prokaryotic genome annotation
-Bioinformatics 2014 Jul 15;30(14):2068-9. PMID:24642063
-
-Dependencies
-------------
-
-Mandatory
-
-- BioPerl
- Used for input/output of various file formats
- Stajich et al, The Bioperl toolkit: Perl modules for the life
- sciences. Genome Res. 2002 Oct;12(10):1611-8.
-
-- GNU Parallel
- A shell tool for executing jobs in parallel using one or more
- computers
- O. Tange, GNU Parallel - The Command-Line Power Tool, ;login: The
- USENIX Magazine, Feb 2011:42-47.
-
-- BLAST+
- Used for similarity searching against protein sequence libraries
- Camacho C et al. BLAST+: architecture and applications. BMC
- Bioinformatics. 2009 Dec 15;10:421.
-
-- Prodigal
- Finds protein-coding features (CDS)
- Hyatt D et al. Prodigal: prokaryotic gene recognition and
- translation initiation site identification. BMC Bioinformatics. 2010
- Mar 8;11:119.
-
-- TBL2ASN Prepare sequence records for Genbank submission Tbl2asn home
- page
-
-Recommended
-
-- Aragorn
- Finds transfer RNA features (tRNA)
- Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and
- tmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004 Jan
- 2;32(1):11-6.
-
-- Barrnap
- Used to predict ribosomal RNA features (rRNA). My licence-free
- replacement for RNAmmmer.
- Manuscript under preparation.
-
-- RNAmmer
- Finds ribosomal RNA features (rRNA)
- Lagesen K et al. RNAmmer: consistent and rapid annotation of
- ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100-8.
-
-- HMMER3
- Used for similarity searching against protein family profiles
- Finn RD et al. HMMER web server: interactive sequence similarity
- searching. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37.
-
-Optional
-
-- SignalP
- Finds signal peptide features in CDS (sig_peptide)
- Petersen TN et al. SignalP 4.0: discriminating signal peptides from
- transmembrane regions. Nat Methods. 2011 Sep 29;8(10):785-6.
-
-- Infernal
- Used for similarity searching against ncRNA family profiles
- D. L. Kolbe, S. R. Eddy. Fast Filtering for RNA Homology Search.
- Bioinformatics, 27:3102-3109, 2011.
-
-
=====================================
doc/update_manual.sh deleted
=====================================
@@ -1,3 +0,0 @@
-#!/bin/sh
-pandoc -f markdown -t plain ../README.md > prokka-manual.txt
-
View it on GitLab: https://salsa.debian.org/med-team/prokka/commit/2537477a4446e8b5afebe76e3bb9c01fe6ba2325
--
View it on GitLab: https://salsa.debian.org/med-team/prokka/commit/2537477a4446e8b5afebe76e3bb9c01fe6ba2325
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20191123/1d70ab0e/attachment-0001.html>
More information about the debian-med-commit
mailing list