Title: PolyLens: software for map-based visualisation and analysis of genome-scale polymorphism data

Authors: Michael W. Berry; Tiantian Gao; Ryhan Pathan; Gary W. Stuart

Addresses: EECS Department, University of Tennessee, Min H. Kao Building, Suite 401, Knoxville, TN 37996, USA ' EECS Department, University of Tennessee, Min H. Kao Building, Suite 401, Knoxville, TN 37996, USA ' EECS Department, University of Tennessee, Min H. Kao Building, Suite 401, Knoxville, TN 37996, USA ' Department of Biology, Indiana State University, 600 Chestnut Street, Terre Haute, IN 47809, USA

Abstract: Software tools for the flexible examination of genomic sequence information derived from populations of organisms in a geospatial context are few in number, closely tied to Web-based resources, generally focused on one or a few loci or haplotypes, and typically produce a global phylogeny as a summary of relatedness. We sought instead to produce a portable, self-contained analysis tool that is efficiently focused on a geospatial display of specifically chosen polymorphism frequencies or combination frequencies from very large data sets of genome-scale sequence from multiple individuals. PolyLens is a Java-based, integral visual analytical toolkit which can systematically process population genomic data, visualise geographic distributions of genealogical lineages, and display allele distribution patterns. PolyLens is designed for users to visualise specific DNA sequences within each individual and its related location information in the existing data set.

Keywords: geographical distributions; genealogical lineages; Java software; nonnegative tensor factorisation; population genomic data; visual analytics; map based visualisation; genome-scale polymorphism data; geospatial display; allele distribution patterns; DNA sequences.

DOI: 10.1504/IJCBDD.2013.052204

International Journal of Computational Biology and Drug Design, 2013 Vol.6 No.1/2, pp.93 - 106

Published online: 20 Feb 2013 *

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