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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

i-rDNA: alignment-free algorithm for rapid in silico detection of ribosomal gene fragments from metagenomic sequence data sets

Monzoorul Haque Mohammed, Tarini Shankar Ghosh, Sudha Chadaram and Sharmila S Mande*

Author Affiliations

Bio-Sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Limited, 1 Software Units Layout, Hyderabad 500 081, Andhra Pradesh, India

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BMC Genomics 2011, 12(Suppl 3):S12  doi:10.1186/1471-2164-12-S3-S12

Published: 30 November 2011

Additional files

Additional File 1:

List of the 112 organisms constituting the simLC, simMC and the simHC data sets along with their representation status with respect to the 55 genomes of training data set.

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Open Data

Additional File 2:

Llist of of 55 organisms used for generating four different training data sets corresponding to the sequence lengths of Sanger, 454-Titanium, 454-Standard, 454-GS20 sequencing technologies.

Format: PDF Size: 93KB Download file

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Open Data

Additional File 3:

The training results obtained using various combinations of 'cumulative sequence count' (20K, 30K 40K, 50K, 60K, 70K, 80K) and 'overlap percentage' (20%, 30%, 40%, 50%, 60%, 70%, 80%). The four tables 3A-D (in this file) show results obtained with Sanger, 454-400, 454-250 and 454-100 training data sets respectively.

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Open Data

Additional File 4:

Summary of the methodology used for computing the true positive/false positive rates and the corresponding analysis on the generated ROC curves

Format: PDF Size: 205KB Download file

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Open Data