IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

small patterns in BLAST or FASTA

Richard Macdonald XXrmacXX at home.com
Thu May 14 00:40:00 EST 1998


Sorry, should have said T and C for Y.

Richard Macdonald wrote:
> 
> 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
> >
> > ******************************************************************************



More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net