Package: wnpp Severity: wishlist Owner: Charles Plessy <[EMAIL PROTECTED]>
Package name : last-align Version : 7 Upstream Author : Martin C. Frith and Paul B. Horton <[EMAIL PROTECTED]> 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, -- Charles -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
