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

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Relation http://oar.icrisat.org/3629/
http://dx.doi.org/10.2390/biecoll-jib-2008-89
 
Title WebStruct and VisualStruct: web interfaces and visualization for Structure software implemented in a cluster environment
 
Creator Jayashree, B.
Rajagopal, S.
Hoisington, D A
et al, .
 
Subject Agriculture-Farming, Production, Technology, Economics
 
Description 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.
 
Publisher http://journal.imbio.de
 
Date 2008
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/3629/1/jib-89.pdf
Jayashree, B. and Rajagopal, S. and Hoisington, D A and et al, . (2008) WebStruct and VisualStruct: web interfaces and visualization for Structure software implemented in a cluster environment. Journal of Integrative Bioinformatics, 5. pp. 1-5. ISSN 1613-4516