Nucleotide Amino Acid Alignment

Nucleotide Amino Acid Alignment (NAP) 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.


Getting Started

If you’re new to NAP, click on the launch button (on the right) and use the Quick Start Page to learn the basics (or if you’re like us…  just start clicking!).

The VBRC also provides additional help resources for NAP:




Huang X, Zhang J.

Methods for comparing a DNA sequence with a protein sequence. Comput Appl Biosci. 1996 Dec;12(6):497-506.



If your system does not launch Viral Orthologous Clusters, it is probably missing Java Runtime Environment 1.7. Please see Java Web Start Setup and Java Web Start Tips for help.


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