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

Jayashree, B.; Hanspal, Manindra S.; Srinivasan, Rajgopal; Vigneshwaran, R.; Varshney, Rajeev K.; Spurthi, N.; Eshwar, K.; Ramesh, N.; Chandra, S.; Hoisington, David A.

doi:https://doi.org/10.1155/2007/35604

International Journal of Genomics

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Research Article | Open Access

Volume 2007 | Article ID 035604 | https://doi.org/10.1155/2007/35604

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

B. Jayashree,¹Manindra S. Hanspal,¹Rajgopal Srinivasan,²R. Vigneshwaran,²Rajeev K. Varshney,³N. Spurthi,³K. Eshwar,³N. Ramesh,⁴S. Chandra,¹and David A. Hoisington³

Academic Editor: Peter Little

Received02 May 2007

Revised20 Jul 2007

Accepted19 Oct 2007

Published02 Dec 2007

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.

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Copyright

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.

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