[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Bug#498562: ITP: last-align -- genome-scale comparison of biological sequences.

Package: wnpp
Severity: wishlist
Owner: Charles Plessy <plessy@debian.org>

  Package name    : last-align
  Version         : 7
  Upstream Author : Martin C. Frith and Paul B. Horton <last@cbrc.jp>
  URL             : http://last.cbrc.jp/
  License         : GPL-3+
  Programming Lang: C++
  Description     : genome-scale comparison of biological sequences.
 LAST is software for comparing and aligning sequences, typically DNA or
 protein sequences. LAST is similar to BLAST, but it copes better with very
 large amounts of sequence data. Here are two things LAST is good at:
  * Comparing large (e.g. mammalian) genomes.
  * Mapping lots of sequence tags onto a genome.
 The main technical innovation is that LAST finds initial matches based on
 their multiplicity, instead of using a fixed size (e.g. BLAST uses 11-mers).
 This allows us to map tags to genomes without repeat-masking, without becoming
 overwhelmed by repetitive hits. To find these variable-sized matches, it uses
 a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a
 discontiguous suffix array, analogous to spaced seeds.

The package is almost ready, but I will wait that GCC 4.3 issues are solved
upstream. Manpages are missing and I will not write some during the freeze.

This package will be part of a larger effort to make Debian the best platform
for large-scale genomics.

Have a nice day,


Reply to: