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

OAR@ICRISAT

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Relation http://oar.icrisat.org/2487/
http://dx.doi.org/10.1155/2007/35604
 
Title An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms
 
Creator Jayashree, B
Hanspal, M S
Srinivasan, R
Vigneshwaran, R
Varshney, R K
Spurthi, N
Eshwar, K
Ramesh, N
Chandra, S
Hoisington, D A
 
Subject Information Science
 
Description 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.
 
Publisher John Wiley & Sons
 
Date 2007
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/2487/1/An_integrated_pipeline_of_open_source_software_adapted_for_multi-CPU_architectures_use_in_the_large-scale_identification_of_single_nucleotide_polymorphisms.pdf
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