Package: wnpp Severity: wishlist Owner: Andreas Tille <ti...@debian.org>
* Package name : blat Version : 35 Upstream Author : Jim Kent <jim_k...@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 -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140303130911.7828.46002.report...@mail.an3as.eu
