[Cdd-commits] r754 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: plessy
Date: Fri May 23 14:28:49 2008
New Revision: 754

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added software for primer design, sequence mapping, and data storage

Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Fri May 23 14:28:49 2008
@@ -1490,3 +1490,39 @@
  Rho-independent transcription terminators illuminates their
  relationship to DNA uptake. Genome Biology 8:R22 (2007).
 Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
+
+Depends: patman
+Homepage: http://bioinf.eva.mpg.de/patman/
+License: GPL-2+
+WNPP: 482555 
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: rapid alignment of short sequences to large databases
+ Patman searches for short patterns in large DNA databases, allowing
+ for approximate matches. It is optimized for searching for many small
+ pattern at the same time, for example microarray probes.
+
+Depends: uniprime
+Homepage: http://code.google.com/p/uniprime/
+License: GPL-3+
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: workflow-based platform for universal primer design
+ UniPrime automatically designs large sets of universal primers by simply
+ inputting a GeneID reference. It automatically retrieves and aligns
+ orthologous sequences from GenBank, identifies regions of conservation within
+ the alignment and generates suitable primers that can amplify variable genomic
+ regions. UniPrime differs from previous automatic primer design programs in
+ that all steps of primer design are automated, saved and are phylogenetically
+ limited. We have experimentally verified the efficiency and success of this
+ program. UniPrime is an experimentally validated, fully automated program that
+ generates successful cross-species primers that take into account the
+ biological aspects of the PCR.
+
+Depends: genetrack
+Homepage: http://sysbio.bx.psu.edu/genetrack.html
+License: MIT
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: genomic data storage and visualization framework
+ GeneTrack is a high performance bioinformatics data storage and analysis
+ system designed to store genome wide information. It is currently used to
+ analyze data obtained via high-throughput rapid sequencing platforms such as
+ the 454 and Solexa as well as tiling array data based on various platforms.