MANTIS, a phylogenetic framework for multi-species genome comparisons

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 mantisdb.org and constitutes the missing link between multi-species genome comparisons and functional analyses.

Helaers, R., Tzika, A., Van de Peer, Y., Milinkovitch, M.C. (2008) MANTIS, a phylogenetic framework for multi-species genome comparisons. Bioinformatics 24(2):151-7.









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