[Cdd-commits] r589 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Mon Mar 10 10:49:28 2008
New Revision: 589

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
More prospective packages from wnpp


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Mon Mar 10 10:49:28 2008
@@ -544,12 +544,77 @@
  in Swiss-Prot or FASTA format. It requires two compiled external
  programs from the PFTOOLS, which are also distributed with the sources.
 
-Depends: 
-Homepage: 
+Depends: proalign
+Homepage: http://evol-linux1.ulb.ac.be/ueg/ProAlign/
 License: GPL
-Pkg-Description:
+Responsible: Charles Plessy <charles-debian-nospam at plessy.org>
+WNPP: 378290
+Pkg-Description: Probabilistic multiple alignment program
+ ProAlign performs probabilistic sequence alignments using hidden Markov
+ models (HMM). It includes a graphical interface (GUI) allowing to (i)
+ perform alignments of nucleotide or amino-acid sequences, (ii) view the
+ quality of solutions, (iii) filter the unreliable alignment regions and
+ (iv) export alignments to other softwares.
+ .
+ ProAlign uses a progressive method, such that multiple alignment is
+ created stepwise by performing pairwise alignments in the nodes of a
+ guide tree. Sequences are described with vectors of character
+ probabilities, and each pairwise alignment reconstructs the ancestral
+ (parent) sequence by computing the probabilities of different
+ characters according to an evolutionary model. It has been published in
+ Bioinformatics. 2003 Aug 12;19(12):1505-13.
 
-Depends: 
-Homepage: 
+Depends: ssaha
+Homepage: http://www.sanger.ac.uk/Software/analysis/SSAHA/
 License: GPL
-Pkg-Description:
+Responsible: Charles Plessy <charles-debian-nospam at plessy.org>
+WNPP: 425111
+Pkg-Description: Sequence Search and Alignment by Hashing Algorithm
+ SSAHA is a software tool for very fast matching and alignment of DNA
+ sequences. It achieves its fast search speed by converting sequence
+ information into a `hash table' data structure, which can then be
+ searched very rapidly for matches. It was published by Ning Z,
+ Cox AJ, Mullikin JC in Genome Res. 2001;11;1725-9.
+ .
+ SSAHA is the only free software of its category (fast search of nearly
+ indentical sequences). The popular alternative, BLAT, is restricted to
+ non-commercial use.
+
+Depends: ngila
+Homepage: http://scit.us/projects/ngila/
+License: GPLv3
+Responsible: Charles Plessy <charles-debian-nospam at plessy.org>
+WNPP: 439996
+Pkg-Description: global pairwise alignments with logarithmic and affine gap costs
+ Ngila is an application that will find the best alignment of a pair
+ of sequences using log-affine gap costs, which are the most
+ biologically realistic gap costs.
+ .
+ Ngila implements the Miller and Myers (1988) algorithm in order to
+ find a least costly global alignment of two sequences given homology
+ costs and a gap cost. Two versions of the algorithm are
+ included: holistic and divide-and-conquer. The former is faster but
+ the latter utilizes less memory. Ngila starts with the
+ divide-and-conquer method but switches to the holistic method for
+ subsequences smaller than a user-established threshold. This improves
+ its speed without substantially increasing memory requirements. Ngila
+ also allows users to assign costs to end gaps that are smaller than
+ costs for internal gaps. This is important for aligning using the
+ free-end-gap method.
+ .
+ Ngila is published in Cartwright RA Bioinformatics 2007
+ 23(11):1427-1428; doi:10.1093/bioinformatics/btm095
+
+Depends: tm-align
+Homepage: http://zhang.bioinformatics.ku.edu/TM-align/
+License: free to change and redistribute
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 447505
+Pkg-Description: structural protein alignment
+ TM-align is a structural alignment program for comparing two proteins
+ whose sequences can be different. TM-align will first find the best
+ equivalent residues of two proteins based on the structure similarity
+ and then output a TM-score.
+ .
+ TM-align performs a structural alignment of protein sequences. It is
+ said to be 10 times faster than DALI and no worse in accuracy.