NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences

Philip L. Tzou, Xiaoqiu Huang, Robert W. Shafer

Current nucleotide-to-amino acid alignment software programs were developed primarily for detecting gene exons within eukaryotic genomes and were therefore optimized for speed across long genetic sequences. We developed a nucleotide-to-amino acid alignment program NucAmino optimized for virus sequencing. NucAmino is an open source program written in the high-level language Go. NucAmino is more likely to align codons flush with a reference sequence's amino acids and can be modified to facilitate the placement of insertions and deletions at specific positions. We compared NucAmino to the nucleotide to amino acid alignment program Local Alignment Program (LAP) using 115,118 human immunodeficiency virus type 1 (HIV-1) protease, reverse transcriptase, and integrase sequences-three genes that are commonly sequenced in clinical laboratories. Discordances between NucAmino and LAP occurred in 512 (16.9%) of the 3,029 sequences containing gaps but in none of 112,910 sequences without gaps. For 242 of the sequences with discordances, NucAmino produced an alignment that was preferable to that found by LAP in that it was more likely to codon align insertions and deletions and to facilitate the placement of an important drug-resistance associated insertion at the position at which most laboratories expect it to occur. NucAmino is a nucleotide-to-amino acid alignment program with several advantages for clinical laboratories performing virus sequencing compared with older programs designed for gene finding.