OrfM: a fast open reading frame predictor for metagenomic data

Woodcroft, Ben J., Boyd, Joel A. and Tyson, Gene W. (2016) OrfM: a fast open reading frame predictor for metagenomic data. Bioinformatics, 32 17: 2702-2703. doi:10.1093/bioinformatics/btw241


Author Woodcroft, Ben J.
Boyd, Joel A.
Tyson, Gene W.
Title OrfM: a fast open reading frame predictor for metagenomic data
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1367-4803
1367-4811
Publication date 2016-05-03
Sub-type Article (original research)
DOI 10.1093/bioinformatics/btw241
Open Access Status DOI
Volume 32
Issue 17
Start page 2702
End page 2703
Total pages 2
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Collection year 2017
Language eng
Abstract Finding and translating stretches of DNA lacking stop codons is a task common in the analysis of sequence data. However the computational tools for finding open reading frames are sufficiently slow that they are becoming a bottleneck as the volume of sequence data grows. This computational bottleneck is especially problematic in metagenomics when searching unassembled reads, or screening assembled contigs for genes of interest. Here we present OrfM, a tool to rapidly identify open reading frames (ORFs) in sequence data by applying the Aho-Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical ORFs to similar tools (‘GetOrf’ and ‘Translate’) but is five times faster. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Chemistry and Molecular Biosciences
 
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Created: Fri, 13 May 2016, 14:39:36 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences