[Debian-med-packaging] Bug#740601: ITP: blat -- BLAST-Like Alignment Tool

[Andreas Tille]

Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille at debian.org>

* Package name    : blat
  Version         : 35
  Upstream Author : Jim Kent <jim_kent at pacbell.net>
* URL             : http://users.soe.ucsc.edu/~kent/src/
* License         : FreeForScientificUse
  Programming Lang: C
  Description     : BLAST-Like Alignment Tool
 BLAT on DNA is designed to quickly find sequences of 95% and greater
 similarity of length 25 bases or more. It may miss more divergent or shorter
 sequence alignments. It will find perfect sequence matches of 25 bases, and
 sometimes find them down to 20 bases. BLAT on proteins finds sequences of 80%
 and greater similarity of length 20 amino acids or more. In practice DNA BLAT
 works well on primates, and protein blat on land vertebrates.
 .
 BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome in
 memory. The index consists of all non-overlapping 11-mers except for those
 heavily involved in repeats. The index takes up a bit less than a gigabyte of
 RAM. The genome itself is not kept in memory, allowing BLAT to deliver high
 performance on a reasonably priced Linux box. The index is used to find areas
 of probable homology, which are then loaded into memory for a detailed
 alignment. Protein BLAT works in a similar manner, except with 4-mers rather
 than 11-mers. The protein index takes a little more than 2 gigabytes.


Remark:  The package is maintained by the Debian Med team at

   git://anonscm.debian.org/debian-med/blat.git