[med-svn] [augustus] 01/10: add manpages contributed by upstream

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
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commit 3d0e9ff1ead87458bbced9b7d902a89a04475983
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu Mar 31 17:45:59 2016 +0000

    add manpages contributed by upstream
---
 debian/mansrc/fastBlockSearch.1.adoc | 50 ++++++++++++++++++++++++++++++++++++
 debian/mansrc/prepareAlign.1.adoc    | 34 ++++++++++++++++++++++++
 2 files changed, 84 insertions(+)

diff --git a/debian/mansrc/fastBlockSearch.1.adoc b/debian/mansrc/fastBlockSearch.1.adoc
new file mode 100644
index 0000000..9a00272
--- /dev/null
+++ b/debian/mansrc/fastBlockSearch.1.adoc
@@ -0,0 +1,50 @@
+# fastBlockSearch(1)
+
+## NAME
+
+fastBlockSearch - search loci matching protein block profiles
+
+## SYNOPSIS
+
+*fastBlockSearch* [options] seqs.fa fam.prfl
+
+## DESCRIPTION
+
+Searches hits (matches) of the blocks in the profile given by fam.prfl within
+the genomic sequences in the file seqs.fa.
+Hits are sorted increasingly by score, so the last displayed hit is the best one
+found in the region. The format is similar to that of the blockscore file (which
+is optionally generated by msa2prfl.pl): It shows coordinate, strand, mean odds-
+ratio score, and specificity of score, and the motif.
+From the output users can chose regions with matching blocks to perform gene
+prediction with AUGUSTUS-PPX using the same block profile.
+
+## OPTIONS
+
+*--cutoff=c*::
+  This minimum for the average log score of the motifs found can be used to adjust the sensitivity of the block search.
+  The standard cutoff is 0.7, which is very sensitive but can give many false positive hits for smaller profiles.
+
+## EXAMPLE
+
+  > fastBlockSearch --cutoff=1.1 chr4.103M.fa PF00225_seed.prfl
+
+  Hits found in chr4 103000000 105000000
+  Score:207.987
+  Mult. score:4.83391
+  1081586 unknown_M[5,13] -       2.32574 5.04633 .....YATRLKNI
+  1103952 unknown_L       -       4.85363 6.75245 NAKTRIICTITP
+  1103991 unknown_K       -       8.38065 9.92928 YRDSKLTRILQNSLG
+  1104375 unknown_J       -       3.96065 6.79408 RSLFILGQVIKKL
+  1106992 unknown_I       -       9.22487 7.64306 LVDLAGSE
+  1115567 unknown_H[5,16] -       2.31869 5.58986 .....ESRHYGETKMN
+  1116319 unknown_G       -       7.34282 8.29425 EIYNETITDLL
+  1117092 unknown_F       -       5.10694 6.10274 VIPRAIHDIF
+  1117146 unknown_E       -       9.43596 9.18891 QTASGKTYTM
+  1117176 unknown_D[1,8]  -       5.73796 6.31532 .GTIFAYG
+  1117399 unknown_B[1,7]  -       3.59083 5.03059 .CLDRVF
+  1119420 unknown_A[0,8]  -       4.64107 6.44285 RVRPLNSR.
+
+## AUTHORS
+
+Oliver Keller
diff --git a/debian/mansrc/prepareAlign.1.adoc b/debian/mansrc/prepareAlign.1.adoc
new file mode 100644
index 0000000..818c5f4
--- /dev/null
+++ b/debian/mansrc/prepareAlign.1.adoc
@@ -0,0 +1,34 @@
+# prepareAlign(1)
+
+## NAME
+
+prepareAlign - prepare an alignment for block profile creation by deleting gap-rich rows
+
+## SYNOPSIS
+
+*prepareAlign* < input.fa  > output.fa
+
+## DESCRIPTION
+
+An input multiple alignment of proteins is read from standard input.
+prepareAlign removes rows from it with the aim of producing fully conserved
+blocks in the remaining alignment which is then output to standard output.
+
+When an alignment contains many sequences and too many gaps, e.g. a full PFAM
+alignment, trying to run msa2prfl.pl results in the message "No blocks found in
+MSA". Then use "prepareAlign" first to eliminate sequences.
+
+## AUTHORS
+
+Oliver Keller
+
+
+
+
+
+
+
+
+
+
+

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