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

BMC Genomics

Proceedings

Monzoorul Haque Mohammed¹  Sudha Chadaram¹  Tarini Shankar Ghosh¹  Sharmila S Mande¹ 

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

关键词: Query Sequence;    rDNA Fragment;    Metagenomic Data;    High Detection Sensitivity;    rDNA Cluster;   

DOI  :  10.1186/1471-2164-12-S3-S12

来源: Springer

【 摘 要 】

BackgroundObtaining accurate estimates of microbial diversity using rDNA profiling is the first step in most metagenomics projects. Consequently, most metagenomic projects spend considerable amounts of time, money and manpower for experimentally cloning, amplifying and sequencing the rDNA content in a metagenomic sample. In the second step, the entire genomic content of the metagenome is extracted, sequenced and analyzed. Since DNA sequences obtained in this second step also contain rDNA fragments, rapid in silico identification of these rDNA fragments would drastically reduce the cost, time and effort of current metagenomic projects by entirely bypassing the experimental steps of primer based rDNA amplification, cloning and sequencing. In this study, we present an algorithm called i-rDNA that can facilitate the rapid detection of 16S rDNA fragments from amongst millions of sequences in metagenomic data sets with high detection sensitivity.ResultsPerformance evaluation with data sets/database variants simulating typical metagenomic scenarios indicates the significantly high detection sensitivity of i-rDNA. Moreover, i-rDNA can process a million sequences in less than an hour on a simple desktop with modest hardware specifications.ConclusionsIn addition to the speed of execution, high sensitivity and low false positive rate, the utility of the algorithmic approach discussed in this paper is immense given that it would help in bypassing the entire experimental step of primer-based rDNA amplification, cloning and sequencing. Application of this algorithmic approach would thus drastically reduce the cost, time and human efforts invested in all metagenomic projects.AvailabilityA web-server for the i-rDNA algorithm is available at http://metagenomics.atc.tcs.com/i-rDNA/

【 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.