Sequences Similar or Chance?

Brian Fristensky frist at
Sun Jan 22 17:22:48 EST 1995

In article 2101951613210001 at, berbee at (Mary Berbee) writes:
> 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).

Bill Pearson's programs prss and rss generate estimates of the likelihood
of a pairwise match by an iterative process of shuffling one sequence and 
determining its similarity score with the other sequence. Shuffling can
be done either globally, or in a sliding window to preserve local
fluctuations in nucleotide or amino acid composition.

These programs are available as part of the FASTA package at

Brian Fristensky                | 
Department of Plant Science     |  Life doesn't imitate art,
University of Manitoba          |  it imitates bad television. 
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