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small patterns in BLAST or FASTA

Tim Cutts tjrc1 at mole.bio.cam.ac.uk
Mon May 11 04:04:36 EST 1998


In article <35544867.275B at courrier.usherb.ca>,
Marco Blanchette  <mblanche at courrier.usherb.ca> wrote:
>I tried to run a blast search with a small nucleic acid patterns against
>all the database. The patterns is 9 nucleotide long with a degenerated
>base (tagaytaga). The output produce no match but i know that there is
>at least 9 sequence that have the patterns. I tried the same thing using
>fasta and again no match were found.
>
>I suspect that my pattern is not long enought but i dont understand why
>I can force the program to find a match.
>
>What's the best way to do that kind of search?

FindPatterns, with the caveat that it won't find copies of the pattern
with insertions or deletions.

Tim.



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