Comparison programs in the FastA3 package
Fasta3 (or gcg�s fasta) - Compare a protein sequence to a protein database, or a DNA sequence to a DNA database, using the fasta algorithm. Search speed and selectivity are controlled with the �ktup� (wordsize) parameter.
Tips for ktup: For proteins, the default, ktup=2, ktup=1 is more sensitive but slower.
For DNA, ktup=6, the default, ktup=3 or ktup=4 more sensitivity, ktup=1 for oligonucleotides (length <20).