Sequences Similar or Chance?

[Peter Myler]

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

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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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