WebStruct and VisualStruct: web interfaces and visualization for Structure software implemented in a cluster environment

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doi doi:10.2390/biecoll-jib-2008-89
submission April 10, 2008
published September 24, 2008
NCBI PubMed PubMed ID 20134055

B. Jayashree, S. Rajgopal, D. Hoisington, V.P. Prasanth and S. Chandra

Correspondence should be addressed to:
B. Jayashree
Bioinformatics Unit, ICRISAT, Patancheru 502324, Andhra Pradeesh, India
gro.raigc@nulleerhsayaj.b


Abstract

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.

Reference

B. Jayashree, S. Rajgopal, D. Hoisington, V.P. Prasanth and S. Chandra. WebStruct and VisualStruct: web interfaces and visualization for Structure software implemented in a cluster environment. Journal of Integrative Bioinformatics, 5(1):89, 2008. Online Journal: http://journal.imbio.de/index.php?paper_id=89
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