small patterns in BLAST or FASTA

William R. Pearson wrp at alpha0.bioch.virginia.edu
Sun May 17 19:51:05 EST 1998

Use FASTA, and specify a wordsize of 1 or 2.  FASTA will find
what you are looking for, and similar sequences as well.  FASTA does use
a default wordsize of 6 for DNA, but it is easily changed.

BLAST does not allow the DNA search wordsize to be changed (I
believe it is 11).

Bill Pearson

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