IUBio

strange behaviour of GCG's fasta

William R. Pearson wrp at alpha0.bioch.virginia.edu
Mon May 13 19:22:31 EST 1996


I believe that the different alignments have different initn scores
because FASTA counts a N:A match as an identity and a N:G as a
non-identity.

The solution is to always do searches with oligonucleotide primers with
ktup=2 or ktup=1; that would fix the problem I think.

Bill Pearson



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