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Bioinformatics Advance Access published online on November 19, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm567
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

MANTIS, a phylogenetic framework for multi-species genome comparisons

Raphaël Helaers 1, Athanasia C. Tzika 1, Yves Van de Peer 2 and Michel C. Milinkovitch 1,*

1 Laboratory of Evolutionary Genetics, Institute for Molecular Biology & Medicine, Université Libre de Bruxelles, 12 rue Jeener & Brachet, B6041 Gosselies, Belgium.
2 Bioinformatics & Evolutionary Genomics, Department of Plant Systems Biology, Ghent University, VIB, Gent, Belgium

*To whom correspondence should be addressed. Prof. Michel C. Milinkovitch1, E-mail: mcmilink{at}ulb.ac.be


  Abstract

Motivation: Practitioners of comparative genomics face huge analytical challenges as whole genome sequences and functional/expression data accumulate. Furthermore, the field would greatly benefit from a better integration of this wealth of data with evolutionary concepts.

Results: Here, we present MANTIS, a relational database for the analysis of (i) gains and losses of genes on specific branches of the metazoan phylogeny, (ii) reconstructed genome content of ancestral species, and (iii) over- or under-representation of functions/processes and tissue specificity of gained, duplicated, and lost genes. MANTIS estimates the most likely positions of gene losses on the true phylogeny using a maximum likelihood function. A user-friendly interface and an extensive query system allow to investigate questions pertaining to gene identity, phylogenetic mapping, and function/expression parameters.

Availability: MANTIS is freely available at http://www.mantisdb.org and constitutes the missing link between multi-species genome comparisons and functional analyses.

Contact: Michel C. Milinkovitch, mcmilink{at}ulb.ac.be

Associate Editor: Prof. Martin Bishop

Received on March 21, 2007; revised on November 7, 2007; accepted on November 8, 2007

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