[Blends-commit] r1911 - projects/med/trunk/debian-med/tasks

[Debian Pure Blends Subversion Commit]

Author: tille
Date: Wed Oct  7 09:02:38 2009
New Revision: 1911
URL: http://svn.debian.org/viewsvn/blends?rev=1911&view=rev

Log:
Added phagefinder


Modified:
   projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=1911&view=diff&r1=1911&r2=1910&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Wed Oct  7 09:02:38 2009
@@ -3044,3 +3044,24 @@
  .
  The source can be downloaded at
  http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip                    
+
+Depends: phagefinder
+Homepage: http://phage-finder.sourceforge.net/
+License: GPL
+Language: Perl
+X-Category: Genomics misc
+Pkg-Description: heuristic computer program to identify prophage regions within bacterial genomes
+ It uses tab-delimited results from NCBI BLASTALL or WU BLASTP 2.0 searches against a
+ collection of bacteriophage protein sequences and results from HMMSEARCH analysis of
+ 441 phage-specific HMMs to locate prophage regions. By using FASTA33, MUMMER  or BLASTN,
+ it can find potential attachment (att) sites of the phage region(s). Data from tRNAscan-SE
+ and Aragorn  are used to determine whether a tRNA  or tmRNA  served as the putative target
+ for integration. Additionally, by looking for the presence or absence of specific proteins
+ using specific HMM models, Phage_Finder can predict whether the region is most likely
+ prophage and which type (Mu, P2, or retron R73), an integrated element, a plasmid, or a
+ degenerate phage region.
+ .
+ The goal of this project is to provide an open-sourced, standardized and automated system
+ to identify and classify prophages within prokaryotic genomes. It is hoped that this package
+ will facilitate future studies on the biology and evolution of these prophages by providing
+ a level of microbial genome annotation that was previously void.