Sequence align. randomizations

Richard P Grant rgrant at worf.molbiol.ox.ac.uk.remove_this_bit
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 
http://worf.molbiol.ox.ac.uk/~rgrant/thesis/4structurestudies.html

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

hth,
Richard

Steve Johnson (sljohnsn at staff.uiuc.edu) 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
http://users.ox.ac.uk/~lady0266    http://www.molbiol.ox.ac.uk/~rgrant
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