NAP (Nucleotide Amino Acid Alignment) is a Java interface to the nap C program. The NAP program computes an optimal global alignment of a DNA sequence and a protein sequence without penalizing terminal gaps. NAP handles frameshifts and long introns in the DNA sequence. It delivers the alignment in linear space, so long sequences can be aligned. The experimental results demonstrate that NAP is a sensitive and powerful tool for finding genes by DNA-protein sequence homology.
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Huang X, Zhang J.
Methods for comparing a DNA sequence with a protein sequence.
Comput Appl Biosci. 1996 Dec;12(6):497-506.