[Cdd-commits] r735 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Thu May  8 07:01:44 2008
New Revision: 735

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added mirbase


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Thu May  8 07:01:44 2008
@@ -1397,19 +1397,22 @@
  part of the AMOS suite.
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
-Depends: velvet
-Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
-License: GPL
-Pkg-Description:
- Velvet is a de novo genomic assembler specially designed for short
- read sequencing technologies, such as Solexa or 454, developed by
- Daniel Zerbino and Ewan Birney at the European Bioinformatics
- Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
+Depends: mirbase
+Homepage: http://microrna.sanger.ac.uk/
+License: Public Domain
+WNPP: 420938
+Responsible: Charles Plessy <charles-debian-nospam at plessy.org>
+Pkg-Description: The microRNA sequence database
+ The miRBase Sequence Database provides a searchable repository
+ for published microRNA sequences and associated annotation,
+ functionality previously provided by the microRNA Registry.  miRBase
+ also contains predicted miRNA target genes in miRBase Targets, and
+ provides a gene naming and nomenclature function in the miRBase
+ Registry.
  .
- Velvet currently takes in short read sequences, removes errors then
- produces high quality unique contigs. It then uses paired read
- information, if available, to retrieve the repeated areas between
- contigs.
-Note: The web site says GPL-3, but the tar archive contains a copy of
- the GPL-2. It also contain a PDF manual whose sources are missing.
- The final package would depend on zlib.
+ Release 9.1 of the database contains 4449 entries representing hairpin
+ precursor miRNAs, expressing 4274 mature miRNA products, in primates,
+ rodents, birds, fish, worms, flies, plants and viruses.
+ .
+ This package will install the miRBase database for mySQL, EMBOSS, and/or
+ ncbi-blast if you have the corresponding packages installed.