Bug#378289: ITP: sigma-align -- Simple greedy multiple alignment of non-coding DNA sequences
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <charles-debian-nospam@plessy.org>
Package name : sigma-align
Version : 1.0
Upstream Author : Rahul Siddharthan <rsidd@imsc.res.in>
URL : http://www.imsc.res.in/~rsidd/sigma/
License : GPL
Description : Simple greedy multiple alignment of non-coding DNA sequences
Sigma ("Simple greedy multiple alignment") is an alignment program with
a new algorithm and scoring scheme designed specifically for non-coding
DNA sequence. It uses a strategy of seeking the best possible gapless
local alignments, at each step making the best possible alignment
consistent with existing alignments, and scores the significance of the
alignment based on the lengths of the aligned fragments and a
background model which may be supplied or estimated from an auxiliary
file of intergenic DNA. With real data, while "correctness" can't be
directly quantified for the alignment, running the PhyloGibbs motif
finder on pre-aligned sequence suggests that Sigma's alignments are
superior. It has been published in BMC Bioinformatics. 2006 Mar
16;7:143.
.
Homepage: http://www.imsc.res.in/~rsidd/sigma/
-- System Information:
Debian Release: testing/unstable
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing')
Architecture: powerpc (ppc64)
Shell: /bin/sh linked to /bin/bash
Kernel: Linux 2.6.16farm
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Reply to: