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.