INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences

BMC Genomics

Proceedings

Monzoorul Haque Mohammed¹  Nitin Kumar Singh¹  Tarini Shankar Ghosh¹  Chennareddy Venkata Siva Kumar Reddy¹  Sharmila S Mande¹  Rachamalla Maheedhar Reddy¹ 

[1] Bio-sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Limited, 1 Software Units Layout, Madhapur, 500081, Hyderabad, Andhra Pradesh, India;

关键词: Taxonomic Level;    Query Sequence;    Reference Database;    Genome Fragment;    Assignment Accuracy;   

DOI  :  10.1186/1471-2164-12-S3-S4

来源: Springer

【 摘 要 】

BackgroundTaxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. Similarity-based approaches, though accurate and specific, are extremely slow. Since, metagenomic projects generate millions of sequences, adopting similarity-based approaches becomes virtually infeasible for research groups having modest computational resources. In this study, we present INDUS - a composition-based approach that incorporates the following novel features. First, INDUS discards the 'one genome-one composition' model adopted by existing compositional approaches. Second, INDUS uses 'compositional distance' information for identifying appropriate assignment levels. Third, INDUS incorporates steps that attempt to reduce biases due to database representation.ResultsINDUS is able to rapidly classify sequences in both simulated and real metagenomic sequence data sets with classification efficiency significantly higher than existing composition-based approaches. Although the classification efficiency of INDUS is observed to be comparable to those by similarity-based approaches, the binning time (as compared to alignment based approaches) is 23-33 times lower.ConclusionGiven it's rapid execution time, and high levels of classification efficiency, INDUS is expected to be of immense interest to researchers working in metagenomics and microbial ecology.AvailabilityA web-server for the INDUS algorithm is available at http://metagenomics.atc.tcs.com/INDUS/

【 授权许可】

Unknown   
© Mohammed et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.