[Biodevelopers] Looking for repeat motifs - ideas?

[J.W. Bizzaro]

Michael,

What threshold would you use for gaps and mismatches?  If you can have any number of mismatches within the motif and any size gap, it becomes more of problem in pattern recognition.

Jeff

Michael Nuhn wrote:
> TTTAAG GCGC TTTAAG
> 
> where the actual sequence of the repeat (TTTAAG) is unknown in advance and
> may have mismatches to the repeat.

-- 
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 508 890 8600
--