Sequence align. randomizations

Richard P Grant rgrant at
Wed Feb 19 05:46:59 EST 1997

Hi Steve,

You want Bill Pearson's rss program.

Can't remember where to get it, but the usual biol places are a good place
to look.

Take a peek at

to see how I used it.  I did 1,000 randomizations - is this sufficient?


Steve Johnson (sljohnsn at 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.

Richard P. Grant  MA  DPhil        University of Oxford
Nuffield Department Obstetrics and Gynaecology      FFPGP
------------------------# "Assimilate THIS!" #------------------------

More information about the Bio-soft mailing list