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Bioinformatics. 2013 Jan 1;29(1):114-6. doi: 10.1093/bioinformatics/bts636. Epub 2012 Nov 4.

MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences.

Author information

1
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Abstract

SUMMARY:

Frameshift (FS) prediction is important for analysis and biological interpretation of metagenomic sequences. Since a genomic context of a short metagenomic sequence is rarely known, there is not enough data available to estimate parameters of species-specific statistical models of protein-coding and non-coding regions. The challenge of ab initio FS detection is, therefore, two fold: (i) to find a way to infer necessary model parameters and (ii) to identify positions of frameshifts (if any). Here we describe a new tool, MetaGeneTack, which uses a heuristic method to estimate parameters of sequence models used in the FS detection algorithm. It is shown on multiple test sets that the MetaGeneTack FS detection performance is comparable or better than the one of earlier developed program FragGeneScan.

AVAILABILITY AND IMPLEMENTATION:

MetaGeneTack is available as a web server at http://exon.gatech.edu/GeneTack/cgi/metagenetack.cgi. Academic users can download a standalone version of the program from http://exon.gatech.edu/license_download.cgi.

PMID:
23129300
PMCID:
PMC3530910
DOI:
10.1093/bioinformatics/bts636
[Indexed for MEDLINE]
Free PMC Article
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