From owner-announce@net.bio.net Wed Oct 14 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Ewan Birney Newsgroups: bionet.announce Subject: Wise2.1.12 beta Date: 15 Oct 1998 10:51:03 -0700 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 46 Sender: daemon@net.bio.net Approved: biosci-help@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Wise 2.1.12 Beta ================ Wise2.1.12 beta is a beta release of the Wise2 package. This package specialises in the comparions of a DNA sequence at the level of its conceptual translation. In the case of genomic DNA a complete gene prediction algorithm is merged with a protein alignment algorithm in genewise. In the case of EST/cDNA DNA, the ability to find frameshifts errors in the DNA sequence is merged with a protein alignment algorithm. The package can compare either protein sequences or profile-HMMs (made by the HMMER package) to DNA sequences. The algorithms can be run in one-on-one modes or database searching modes. In the database search, a profile-HMM database can be used, such as those produced by Pfam. The source code can be downloaded by anonymous ftp from ftp://ftp.sanger.ac.uk/pub/birney/wise2 in wise2.1.12.tar.gz or in binary format as ftp://ftp.sanger.ac.uk/pub/birney/wise2/binaries More information on Wise2, including web forms to try the algorithms out can be found at http://www.sanger.ac.uk/Software/Wise2/ The functionality of the programs can be accessed via a Perl port to the package, or a C API. Contact birney@sanger.ac.uk for more information or read the web site http://www.sanger.ac.uk/Software/Wise2/Programming/ Ewan Birney http://www.sanger.ac.uk/Users/birney/ .