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Bioinformatics Advance Access published online on March 24, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm038
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MPP: A Microarray-To-Phylogeny Pipeline for Analysis of Gene and Marker Content Datasets

Robert Davey 1,2,*, George Savva 2, Jo Dicks 2 and Ian N. Roberts 1

1National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK and 2Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

*To whom correspondence should be addressed. Robert Davey, E-mail: robert.davey{at}bbsrc.ac.uk


  Abstract

Summary: MPP is a Java application, encompassing both new and established algorithms, for the analysis of gene and marker content datasets arising from high-throughput microarray techniques. MPP analyses flat file output from microarray experiments to determine the probability of the presence or absence of genes or markers within a genome. MPP can construct gene or marker content datasets for a number of genomes and can use the data to estimate an evolutionary tree or network. Results from gene content analyses may be validated by comparing them to known gene contents. MPP was initially developed to analyse data derived from Comparative Genome Hybridisation (CGH) microarray experiments in fungi and bacteria. It has recently been adapted to analyse retrotransposon-based insertion polymorphism (RBIP) marker scores derived from tagged microarray marker (TAM) experiments in pea. New analytical procedures may be added easily to MPP as plugins in order to increase the scope of the software.

Availability: MPP source code, executables and online help are available at http://cbr.jic.ac.uk/dicks/software/.

Associate Editor: Dr. Chris Stoeckert

Received on June 30, 2006; revised on January 29, 2007; accepted on January 30, 2007

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