Help with searching an oligonucleotide database

Ashok Aiyar aiyar at ebv.oncology.wisc.edu
Thu Jun 10 21:15:10 EST 1999


I have a large number of oligonucleotide sequences available as
as fasta format database.  These oligos range in length from 15
nucleotides to about 100 nucleotides.  

I would like to search a larger sequence (3 - 5 kb) against this 
database -- so that I can identify all the oligos that lie in the 
large sequence, and use them as PCR primers or whatever.

What publically available programs are suitable for this search? 
I have tried using Bill Pearson's fasta or ssearch programs, but 
they appear unsuitable (or I don't know what command line parameters 
to pass).  Fasta/ssearch find both perfect and imperfect matches,
while I would like to find perfect matches over the entire length
of the oligonucleotide.

Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar at ebv.oncology.wisc.edu

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