If Paul is right, you should be able to run two blast
searches by substituting A and C for the Y,
and pool the results. Or write a perl script to do it
automatically.
--richard
Paul Roy wrote:
>> 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
>> ******************************************************************************
