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.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Copyright Owner
The Authors
Copyright Date
2017
Language
en
File Format
application/pdf
Recommended Citation
Tzou, Philip L.; Huang, Xiaoqiu; and Shafer, Robert W., "NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences" (2017). Computer Science Publications. 21.
https://lib.dr.iastate.edu/cs_pubs/21
Included in
Biochemistry, Biophysics, and Structural Biology Commons, Bioinformatics Commons, Computer Sciences Commons, Genetics and Genomics Commons
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.