Campus Units

Computer Science

Document Type

Article

Publication Version

Published Version

Publication Date

2017

Journal or Book Title

BMC Bioinformatics

Volume

18

First Page

138

DOI

10.1186/s12859-017-1555-6

Abstract

Background

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.

Results

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.

Conclusions

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.

Comments

This article is published as Tzou, Philip L., Xiaoqiu Huang, and Robert W. Shafer. "NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences." BMC bioinformatics 18 (2017): 138. doi: 10.1186/s12859-017-1555-6.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

Copyright Owner

The Authors

Language

en

File Format

application/pdf

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