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small patterns in BLAST or FASTA

Marco Blanchette mblanche at courrier.usherb.ca
Sat May 9 07:13:27 EST 1998


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?

Marco
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Marco Blanchette

mblanche at courrier.usherb.ca

Laboratoire Dr. B. Chabot
Departement de microbiologie et d'infectiologie
Faculte de medecine, CUSE site Fleurimont
Universite de Sherbrooke
Sherbrooke (Quebec)
Canada
J1H 5N4

Tel: (819) 564-5321
Fax: (819) 564-5392
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