On Sat, 9 May 1998, Marco Blanchette 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.
Both Blast and Fasta first try to find exact word-matches of 5-6 nt. The
central Y in your sequence means that there will be no exact matching
words to your input sequence. Ambiguities are OK in long sequences to
score the alignments but do not contribute to word counts in the initial
step.
> What's the best way to do that kind of search? >
Findpatterns as Tim Cutts suggested.
Salut bien,
Paul
******************************************************************************
Paul H. Roy Phone: +1 418 654 2705
Departement de biochimie,FSG FAX: +1 418 654 2715
Universite Laval E-mail: proy at rsvs.ulaval.ca
Quebec, QC G1K 7P4
CANADA
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