[med-svn] r13825 - trunk/packages/microbiomeutil/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-06-04 09:45:16 +0000 (Tue, 04 Jun 2013)
New Revision: 13825

Modified:
   trunk/packages/microbiomeutil/trunk/debian/changelog
   trunk/packages/microbiomeutil/trunk/debian/control
Log:
Enhance long descriptions


Modified: trunk/packages/microbiomeutil/trunk/debian/changelog
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/changelog	2013-06-04 09:25:43 UTC (rev 13824)
+++ trunk/packages/microbiomeutil/trunk/debian/changelog	2013-06-04 09:45:16 UTC (rev 13825)
@@ -9,6 +9,7 @@
      - Debhelper 9 (also d/compat)
      - Dropped explicit quilt Build-Dependends
      - better formatting
+     - Enhance long descriptions
   * debian/rules: remove "--with quilt" because this is specified in
     source format
   * debian/rules, debian/*.install, debian/*.links:

Modified: trunk/packages/microbiomeutil/trunk/debian/control
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/control	2013-06-04 09:25:43 UTC (rev 13824)
+++ trunk/packages/microbiomeutil/trunk/debian/control	2013-06-04 09:45:16 UTC (rev 13825)
@@ -32,10 +32,30 @@
 Depends: ${misc:Depends},
          microbiomeutil-data,
          cdbfasta
+Recommends: nast-ier
 Description: detects likely chimeras in PCR amplified DNA
- ChimeraSlayer is from the microbiomeutil package.
+ ChimeraSlayer is a chimeric sequence detection utility, compatible with
+ near-full length Sanger sequences and shorter 454-FLX sequences (~500bp).
  .
- http://microbiomeutil.sourceforge.net/#A_CS
+ Chimera Slayer involves the following series of steps that operate to
+ flag chimeric 16S rRNA sequences:
+ .
+  1. the ends of a query sequence are searched against an included
+     database of reference chimera-free 16S sequences to identify potential
+     parents of a chimera
+  2. candidate parents of a chimera are selected as those that form a
+     branched best scoring alignment to the NAST-formatted query sequence
+  3. the NAST alignment of the query sequence is improved in a
+     ‘chimera-aware’ profile-based NAST realignment to the selected
+     reference parent sequences
+  4. an evolutionary framework is used to flag query sequences found to
+     exhibit greater sequence homology to an in silico chimera formed
+     between any two of the selected reference parent sequences.
+ .
+ To run Chimera Slayer, you need NAST-formatted sequences generated by
+ the nast-ier utility.
+ .
+ ChimeraSlayer is part of the microbiomeutil suite.
 
 Package: nast-ier
 Architecture: any
@@ -44,23 +64,46 @@
          microbiomeutil-data,
          cdbfasta
 Description: NAST-based DNA alignment tool
- NAST-iEr is from the microbiomeutil package.
+ The NAST-iEr alignment utility aligns a single raw nucleotide sequence 
+ against one or more NAST formatted sequences.
  .
- http://microbiomeutil.sourceforge.net/#A_NASTiEr
+ The alignment algorithm involves global dynamic programming profile 
+ alignment to fixed (NAST-formatted) multiply aligned template sequences
+ without any end-gap penalty.
+ .
+ NAST-iEr is part of the microbiomeutil suite.
 
 Package: wigeon
 Architecture: all
 Depends: ${misc:Depends},
          microbiomeutil-data
+Recommends: nast-ier
 Description: reimplementation of the Pintail 16S DNA anomaly detection utility
- WigeoN is from the microbiomeutil package
+ WigeoN examines the sequence conservation between a query and a trusted
+ reference sequence, both in NAST alignment format. Based on the sequence
+ identity between the query and the reference sequence, there is an
+ expected amount of variation among the alignment. If the observed
+ variation is greater than the 95% quantile of the distribution of
+ variation observed between non-anomalous sequences, then it is flagged
+ as an anomaly.
  .
- http://microbiomeutil.sourceforge.net/#A_WigeoN
+ WigeoN is a flexible command-line based reimplementation of the Pintail
+ algorithm Appl Environ Microbiol. 2005 Dec;7112:7724-36.
+ .
+ WigeoN is useful for flagging chimeras and anomalies only in near
+ full-length 16S rRNA sequences. WigeoN lacks sensitivity with sequences
+ less than 1000 bp.
 
+ To run WigeoN, you need NAST-formatted sequences generated by the
+ nast-ier utility.
+ .
+ WigeoN is  part of the microbiomeutil suite.
+
 Package: microbiomeutil-data
 Architecture: all
 Depends: ${misc:Depends}
+Enhances: chimeraslayer, nast-ier, wigeon
 Description: Reference 16S sequences and NAST-alignments used by microbiomeutil tools
- Reference data for tools in the microbiomeutil package.
- .
- http://microbiomeutil.sourceforge.net
+ Reference data for tools in the microbiomeutil package.  The algorithms
+ used by the tools chimeraslayer, nast-ier and wigeon are based on
+ reference data which are provided by this package.