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Bioinformatics Advance Access published online on October 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti060
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 25, 2004
Revised June 29, 2004
Accepted July 7, 2004

Applications note

ParIS genome rearrangement server

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

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

* To whom correspondence should be addressed. E-mail: miklosi{at}ramet.elte.hu.


  Abstract

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 to another, length distribution of mutations, number of mutations happened at a given site. Both text and graphical outputs are available. We provide a limited server, a downloadable unlimited server which 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.


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