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