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Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Bioinformatics 2016 ; 32 (17): 2702-3 Nephropedia Template TP
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OrfM: a fast open reading frame predictor for metagenomic data #MMPMID27153669
Woodcroft BJ; Boyd JA; Tyson GW
Bioinformatics 2016[Sep]; 32 (17): 2702-3 PMID27153669show ga
Summary: 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 four-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.Availability and Implementation: Source code and binaries are freely available for download at http://github.com/wwood/OrfM or through GNU Guix under the LGPL 3+ license. OrfM is implemented in C and supported on GNU/Linux and OSX.Contacts:b.woodcroft@uq.edu.auSupplementary information:Supplementary data are available at Bioinformatics online.
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free
free
Bioinformatics 2016 ; 32 (17): 2702-3
