Wise2.0 beta release

Ewan Birney birney at sanger.ac.uk
Fri Feb 27 07:53:15 EST 1998

Wise2.0 beta release

Wise2 is the new package which builds on the old concepts
of Wisetools to provide DNA comparisons at the conceptual
level of proteins.

A web page desrcibing the package is available at:


A web server providing an interface to the programs
is available at


Wise2.0 has a number of features which show marked improvement
over the old package:

  1) The GeneWise algorithms, which can compare protein information
     directly to genomic DNA sequence, on-the-fly gene predicting
     are available.

     These algorithms can be parameterised for human or worm sequences.

  2) The package is compatible with the HMMer (Sean Eddy) profile-HMM
     package for describing protein domains. This means that
     from, for example, Pfam can be used to compare against genomic DNA

     For more information on HMMer see


     For more information on Pfam see


  3) A C-program, postwise, is provided for large-scale analysis to
     the application of genewise alignments from a BLASTX analysis.

  4) The protein vs cDNA algorithm has been upgraded to work with HMMer

  5) The programs can now do alignments in much less memory (under 1Mb).
     If you have the memory however, it can take advantage of that as

  6) The entire package has been rewritten using Dynamite. This provides
     a much more consistent memory management, better error handling and
     the chance of a consistent C-based API to the package. This API is
     namespace protected so that it can be linked to other packages
     name clashes (hopefully!).

  7) There is more documentation and the documentation of the code is

On the down side, the database searching modes of the algorithms have
made it through to even external alpha testing, but this will happen

Wise2.0.3 is now ready for beta testing. You can pick it up from


as wise2.0.3b.tar

(if you pick up wise2.0.3b.tar.Z it will on-the-fly compress it).

The tar file contains a mirror of the Web site listed above.

Wise2.0 is freely distributed under a Gnu public license (see tar file
GNULICENSE for more details) and includes other GPL code from Sean Eddy.

There is a bounty for bugs and suggestions. I'm giving away a crate
of beer for the best tester of the programs (to be awarded at ISMB 98).
Hopefully this will encourage you to send in bugs and suggestions.

Mail them to birney at sanger.ac.uk...

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