small patterns in BLAST or FASTA

Paul Roy proy at rsvs.ulaval.ca
Mon May 11 09:02:51 EST 1998

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

> What's the best way to do that kind of search? > 

Findpatterns as Tim Cutts suggested.

Salut bien,



 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


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