MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences

• Type of Material: Article
• Authors: Shiyuyun Tang, Georgia Institute of Technology; Ivan Antonov, Georgia Institute of Technology; Mark Borodovsky, Emory University
• Language: English
• Date: 2013-01-01
• Publisher: Oxford University Press (OUP)
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2012. Published by Oxford University Press.
• License: Creative Commons Attribution 3.0 Unported
• Final Published Version (URL): http://dx.doi.org/10.1093/bioinformatics/bts636
• Title of Journal or Parent Work: Bioinformatics
• ISSN: 1367-4803
• Volume: 29
• Issue: 1
• Start Page: 114
• End Page: 116
• Grant/Funding Information: This work was supported in part by NIH grant HG00783 to M.B.
• Keywords: PREDICTION; Technology; Mathematical & Computational Biology; Science & Technology; Biotechnology & Applied Microbiology; Statistics & Probability; Computer Science; IDENTIFICATION; Mathematics; Biochemistry & Molecular Biology; GENE; BIOTECHNOLOGY & APPLIED MICROBIOLOGY; BIOCHEMICAL RESEARCH METHODS; MATHEMATICAL & COMPUTATIONAL BIOLOGY; Computer Science, Interdisciplinary Applications; Life Sciences & Biomedicine; Biochemical Research Methods; Physical Sciences
• Research Categories: Engineering, Biomedical; Biology, Bioinformatics

Abstract

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.