Sequences Similar or Chance?

Bill Pearson wrp at
Fri Jan 27 11:22:06 EST 1995

In article <Pine.A32.3.91c.950123112943.26162A-100000 at>,
Peter Myler  <mylerpj at> wrote:
>On 22 Jan 1995, Mary Berbee wrote:
>> We are looking for a program to tell us if two sequences are likely to be
>> similar by chance or by homology.  I assume there would be a method by
>> randomly shuffling the bases (ie, keeping the base ratio the same but
>> randomizing their order, then comparing the percent remaining the same
>> when aligned).
>There is a DOS program called RDF2 which does pretty much what you have 
>described.  It used a FASTA type alignment, I believe.  I don't know 
>where to get it on the NET,

Unix, DOS, and Mac versions of the FASTA package is available via
anonymous FTP from in pub/fasta.  The unix version has
improved shuffling/significance programs, prss and prdf, which
calculate an expectation based on the distribution of shuffled
sequence scores and the extreme value distribution.  Unfortunately,
these have not been included in the DOS and Mac versions yet.

Bill Pearson
wrp at virginia.EDU
Dept. of Biochemistry #440
U. of Virginia
Charlottesville, VA 22908

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