MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences

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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.

Contact:borodovsky@gatech.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

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