| WebStruct and VisualStruct: Web interfaces and visualization for Structure software implemented in a cluster environment. | |
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MedLine Citation:
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PMID: 20134055 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Structure, is a widely used software tool to investigate population genetic structure with multi-locus genotyping data. The software uses an iterative algorithm to group individuals into "K" clusters, representing possibly K genetically distinct subpopulations. The serial implementation of this programme is processor-intensive even with small datasets. We describe an implementation of the program within a parallel framework. Speedup was achieved by running different replicates and values of K on each node of the cluster. A web-based user-oriented GUI has been implemented in PHP, through which the user can specify input parameters for the programme. The number of processors to be used can be specified in the background command. A web-based visualization tool "Visualstruct", written in PHP (HTML and Java script embedded), allows for the graphical display of population clusters output from Structure, where each individual may be visualized as a line segment with K colors defining its possible genomic composition with respect to the K genetic sub-populations. The advantage over available programs is in the increased number of individuals that can be visualized. The analyses of real datasets indicate a speedup of up to four, when comparing the speed of execution on clusters of eight processors with the speed of execution on one desktop. The software package is freely available to interested users upon request. |
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Authors:
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B Jayashree; S Rajgopal; D Hoisington; V P Prasanth; S Chandra |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2008-09-24 |
Journal Detail:
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Title: Journal of integrative bioinformatics Volume: 5 ISSN: 1613-4516 ISO Abbreviation: J Integr Bioinform Publication Date: 2008 |
Date Detail:
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Created Date: 2010-02-05 Completed Date: 2010-04-16 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101503361 Medline TA: J Integr Bioinform Country: Germany |
Other Details:
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Languages: eng Pagination: - Citation Subset: IM |
Affiliation:
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Bioinformatics Unit, ICRISAT, Patancheru 502324, Andhra Pradeesh, India. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms Alleles Cluster Analysis Computational Biology Computer Graphics Gene Frequency Genetics, Population Genome Genotype Humans Internet Markov Chains Monte Carlo Method Software* User-Computer Interface* |
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