Table of Contents Author Guidelines Submit a Manuscript
Comparative and Functional Genomics
Volume 2007, Article ID 35604, 7 pages
http://dx.doi.org/10.1155/2007/35604
Research Article

An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms

1Bioinformatics Unit, GT-Biotechnology, International Corps Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
2Advanced Technology Centre, Tata Consultancy Services, Madhapur, Hyderabad 500081, India
3Applied Genomics Laboratory, GT-Biotechnology, International Corps Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
4Novell IDE, Bangalore 560068, India

Received 2 May 2007; Revised 20 July 2007; Accepted 19 October 2007

Academic Editor: Peter Little

Copyright © 2007 B. Jayashree et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.