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small patterns in BLAST or FASTA

Richard Macdonald XXrmacXX at home.com
Thu May 14 00:08:17 EST 1998


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
> 
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