Sequences Similar or Chance?
mylerpj at u.washington.edu
Mon Jan 23 14:31:40 EST 1995
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).
> Any suggestions on this will be greatly appreciated!
> Dave Carmean carmean at sfu.ca
> Mary Berbee berbee at unixg.ubc.ca
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, but I have a copy which I can send if you
want to e-mail me.
Peter J. Myler phone: (206) 284-8846x332
Seattle Biomedical Research Institute FAX: (206) 284-0313
4 Nickerson Street e-mail: MYLERPJ at U.WASHINGTON.EDU
Seattle, WA 98109-1651
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