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

Hindawi Publishing Corporation Comparative and Functional Genomics Volume 2007, Article ID 35604, 7 pages doi: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 B. Jayashree,1 Manindra S. Hanspal,1 Rajgopal Srinivasan,2 R. Vigneshwaran,2 Rajeev K. Varshney,3 N. Spurthi,3 K. Eshwar,3 N. Ramesh,4 S. Chandra,1 and David A. Hoisington3 1 Bioinformatics Unit, GT-Biotechnology, International Corps Research Institute for the Semi-Arid Tropics, Patancheru 502324, India 2 Advanced Technology Centre, Tata Consultancy Services, Madhapur, Hyderabad 500081, India 3 Applied Genomics Laboratory, GT-Biotechnology, International Corps Research Institute for the Semi-Arid Tropics, Patancheru 502324, India 4 Novell IDE, Bangalore 560068, India Correspondence should be addressed to B. Jayashree, b.jayashree@ Received 2 May 2007; Revised 20 July 2007; Accepted 19 October 2007 Recommended by Peter Little 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 softwa