From owner-announce@net.bio.net Wed Apr 14 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Ewan Birney Newsgroups: bionet.announce Subject: Wise2 beta release Date: 15 Apr 1999 13:35:21 -0700 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 88 Sender: daemon@net.bio.net Approved: kristoff@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Wise2 beta release ================== The Wise2 package has a new beta release (2.1.17). Wise2 is a package which specialises in comparisons of DNA sequences at the level of their conceptual translation. Wise2 can be used to o Search a protein sequence against an EST database without concern to sequencing errors o Search a genomic DNA sequence against a library of protein profile-HMMs without needing to predict the genes in the DNA sequence o Many other combinations of similarly minded algorithms. A web site of the Wise2 package is at http://www.sanger.ac.uk/Software/Wise2 It contains documentation, download instructions and web forms to try the algorithms out on your own sequences. Wise2 is available as source code, licensed under GPL, which means it is freely available to everyone. Wise2 works in harmony with the HMMER package by Sean Eddy and the Pfam database from the Pfam consortium. A full list of features of the 2.1.17 compared to the 2.1.16 release are below + Documentation o Documentation has been expanded with a view of the practical use of the programs + Algorithmic o a protein vs protein database search program is provided by Richard Copley. This program includes - Extreme Value Distribution fitting (from Sean Eddy's libraries) - The 'generalised gap penalty' model (abc model) described by stephen altschul o The genewise algorithms now prevent matches occurring in long N repeats (figuring that they are repeats) o The genewise/genewisedb programs can automatically flag potential pseudogenes o The genewise/genewisedb programs can be used without considering introns (useful for bacterial genomic DNA). o Protein translations 'fixed' over frameshifts are now accessible o The estwisedb program can provide protein multiple alignments when a single HMM is used to search a EST database + Programmatic o All the database searching code can be used on SMP boxes (pthread port) stably o A stable Perl port via the XS layer can be used to access the functionality of the Wise2 package directly from Perl o A number of scripts that use the perl port are provided in the distribution o Many minor bugs have been excised The Wise2 package is maintained by Ewan Birney, who is the main author of it. The pswdb program was provided by Richard Copley. Many other testers have provided invaluable feedback, in particular Doug Rusch, Erik Sonnhammer, James Cuff, Valerie Wood and Michele Clamp. Ewan Birney http://www.sanger.ac.uk/Users/birney/ .