Wise2 beta release

Ewan Birney birney at sanger.ac.uk
Fri Apr 9 13:31:55 EST 1999

    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


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

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

  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

  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
<birney at sanger.ac.uk>

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