Sequence align. randomizations

Geoff Barton gjb at
Wed Feb 26 12:19:58 EST 1997

Steve Johnson wrote:
> Can anyone suggest a program that will calculate a "similarity" value
> for two protein sequences and then randomize one sequence and
> recalculate the similarity. I need to generate some good statistical
> values for some fairly similar sequences. I know that GCG's bestfit will
> do this however, I would like to get more than 100 randomizations.
> Thanks.
> Steve Johnson
> sljohnsn at

The AMPS package will do this.  See our WWW and ftp site for details.

Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of
Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K.
mailto:geoff.barton at, Tel: +44 1865 275368, Fax: +44 1865

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