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Bioinformatics Advance Access originally published online on November 19, 2007
Bioinformatics 2008 24(2):151-157; 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

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

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

*To whom correspondence should be addressed.


  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: mcmilink{at}ulb.ac.be

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Martin Bishop

Received on September 22, 2007; revised on November 7, 2007; accepted on November 7, 2007

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