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This article is part of the supplement: Tenth International Conference on Bioinformatics. First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011): Computational Biology

Open Access Proceedings

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

Monzoorul Haque Mohammed, Tarini Shankar Ghosh, Rachamalla Maheedhar Reddy, Chennareddy Venkata Siva Kumar Reddy, Nitin Kumar Singh and Sharmila S Mande*

Author Affiliations

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

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BMC Genomics 2011, 12(Suppl 3):S4  doi:10.1186/1471-2164-12-S3-S4

Published: 30 November 2011

Additional files

Additional file 1:

Threshold determination and parameter optimization A document describing the following: a. The methodology used for obtaining distance threshold values for identifying an appropriate taxonomic level of assignment. b. The methodology adopted for characterization of parameters for the logarithmic normalization. c. Validation of the efficiency of normalization procedure. d. The methodology for the assignment of taxa to query sequences.

Format: PDF Size: 630KB Download file

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Open Data

Additional file 2:

List of organisms constituting the four test data sets A document containing the list constituting the four simulated test data sets and their status with respect to the modified reference database.

Format: PDF Size: 61KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

List of organisms constituting the FAMeS data sets. A document containing the list constituting the simHC, simMC and the simLC data sets and their status with respect to the modified reference database.

Format: PDF Size: 84KB Download file

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Open Data

Additional File 4:

Detailed results of validation on the simulated test data sets A document summarizing the pattern of taxonomic assignments and the time taken by INDUS, TACOA, SOrt-ITEMS, MEGAN and SPHINX on the four simulated test data sets.

Format: PDF Size: 60KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Time performance of the INDUS algorithm A document containing the time taken by INDUS for binning 10000, 20000, 100000 and 500000 sequences.

Format: PDF Size: 37KB Download file

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Open Data

Additional File 6:

Detailed results of validation on the FAMeS data sets A document containing the summarized results of (A) INDUS (B) TACOA (C)SOrt-ITEMS (D) MEGAN and (E) SPHINX obtained for the simLC, simMC and simHC data sets.

Format: PDF Size: 63KB Download file

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Open Data

Additional File 7:

Probable taxonomic assignment patterns for Horizontal Gene Transfer (HGT) regions A document summarizing the probable pattern of taxonomic assignment (obtained using INDUS and a 'one-genome-one-composition' model based method) for sequences that originate from genomic regions involved in lateral gene transfer events.

Format: PDF Size: 26KB Download file

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Open Data

Additional File 8:

Similarities/dissimilarities between INDUS and SPHINX A document summarizing the similarities/dissimilarities in the overall taxonomic assignment procedure adopted by INDUS and SPHINX.

Format: PDF Size: 35KB Download file

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Open Data