Wise 2.1.12 Beta
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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 at sanger.ac.uk for more
information or read the web site
http://www.sanger.ac.uk/Software/Wise2/Programming/
Ewan Birney
<birney at sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/
