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Bioinformatics Advance Access originally published online on October 12, 2004
Bioinformatics 2005 21(6):817-820; doi:10.1093/bioinformatics/bti060
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

ParIS Genome Rearrangement server

I. Miklós 1,*, P. Ittzés 2 and J. Hein 3

1Theoretical Biology and Ecology Modelling Group, Hungarian Academy of Sciences and Eötvös Loránd University Pázmány Péter Sétány 1/c. H-1117 Budapest, Hungary
2Collegium Budapest, Institute for Advanced Study Szentháromság u. 2. H-1014 Budapest, Hungary
3Genome Analysis and Bioinformatics Group, Oxford Centre for Gene Function, Department of Statistics, Oxford University 1 South Parks Road, Oxford OX1 3TG, UK

*To whom correspondence should be addressed.

Summary: ParIS Genome Rearrangement is a web server for a Bayesian analysis of unichromosomal genome pairs. The underlying model allows inversions, transpositions and inverted transpositions. The server generates a Markov chain using a Partial Importance Sampler technique, and samples trajectories of mutations from this chain. The user can specify several marginalizations to the posterior: the posterior distribution of number of mutations needed to transform one genome into another, length distribution of mutations, number of mutations that have occurred at a given site. Both text and graphical outputs are available. We provide a limited server, a downloadable unlimited server that can be installed locally on any linux/Unix operating system, and a database of mitochondrial gene orders.

Availability: http://www.colbud.hu:8765/paris.html and http://doob.stats.ox.ac.uk/~miklos/paris.html

Contact: miklosi{at}ramet.elte.hu


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