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

    Jayashree, B and Hanspal, M S and Srinivasan, R and Vigneshwaran, R and Varshney, R K and Spurthi, N and Eshwar, K and Ramesh, N and Chandra, S and Hoisington, D A (2007) An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms. Comparative and Functional Genomics (35604). pp. 1-7. ISSN 1531-6912

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    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.

    Item Type: Article
    Divisions: UNSPECIFIED
    CRP: UNSPECIFIED
    Subjects: Others > Information Science
    Depositing User: Mr Sanat Kumar Behera
    Date Deposited: 14 Oct 2011 06:31
    Last Modified: 14 Oct 2011 06:31
    URI: http://oar.icrisat.org/id/eprint/2487
    Official URL: http://dx.doi.org/10.1155/2007/35604
    Projects: UNSPECIFIED
    Funders: Generation Challenge Program
    Acknowledgement: The authors gratefully acknowledge financial support though the Generation Challenge Program for the high perfomance computing facility and software tools development
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