Bug#740601: ITP: blat -- BLAST-Like Alignment Tool
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>
* Package name : blat
Version : 35
Upstream Author : Jim Kent <jim_kent@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
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