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Bioinformatics Advance Access originally published online on May 13, 2009
Bioinformatics 2009 25(14):1722-1730; doi:10.1093/bioinformatics/btp317
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

M. Monzoorul Haque {dagger}, Tarini Shankar Ghosh {dagger}, Dinakar Komanduri and Sharmila S. Mande *

Bio-Sciences Division, Innovation Laboratory, Tata Consultancy Services Limited, 1 Software Units Layout, Madhapur, Hyderabad 500 081, India

* To whom correspondence should be addressed.


  Abstract

Motivation:One of the first steps in metagenomic analysis is the assignment of reads/contigs obtained from various sequencing technologies to their correct taxonomic bins. Similarity-based binning methods assign a read to a taxon/clade, based on the pattern of significant BLAST hits generated against sequence databases. Existing methods, which use bit-score as the sole parameter to ascertain the significance of BLAST hits, have limited specificity and accuracy of binning. A new binning algorithm, called SOrt-ITEMS is introduced, which addresses these limitations. The method uses alignment parameters besides the bit score to first identify an appropriate taxonomic level where the read can be assigned. An orthology-based approach is subsequently used by the method for the final assignment.

Results:The performance of SOrt-ITEMS has been validated with reads simulating sequences from 454 and Sanger sequencing technologies. In addition, the taxonomic composition of the Sargasso Sea data set has been analyzed using SOrt-ITEMS. SOrt-ITEMS shows improved specificity and accuracy of assignments especially in simulated scenarios, wherein sequences corresponding to the source organism of the reads are absent in the reference database.

Availability:SOrt-ITEMS software is available for download from: http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS. No license is needed for academic and nonprofit use.

Contact: sharmila{at}atc.tcs.com

Supplementary information:Supplementary data are available at Bioinformatics online.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Alex Bateman

Received on February 24, 2009; revised on May 11, 2009; accepted on May 11, 2009

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