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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
MANTIS: a phylogenetic framework for multi-species genome comparisons
Athanasia C Tzika1, Raphaël Helaers, Yves Van de Peer
1Laboratory of Evolutionary Genetics, Institute for Molecular Biology & Medicine, Université Libre de Bruxelles, Belgium.
Bioinformatics (Oxford, England)
|November 21, 2007
Summary
This study introduces MANTIS, a novel database integrating comparative genomics and evolutionary concepts. It analyzes gene dynamics and ancestral genomes, bridging multi-species comparisons with functional insights.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Comparative genomics presents significant analytical challenges due to accumulating sequence and functional data.
- Integrating vast genomic datasets with evolutionary concepts is crucial for advancing the field.
Purpose of the Study:
- To present MANTIS, a relational database designed for comprehensive analysis of genomic data.
- To facilitate the study of gene gains and losses, ancestral genome reconstruction, and functional/tissue specificity analysis within evolutionary frameworks.
Main Methods:
- Developed MANTIS, a relational database with a user-friendly interface and extensive query system.
- Employed a maximum-likelihood function to estimate the most probable locations of gene losses on phylogenetic trees.
Main Results:
- MANTIS enables analysis of gene gains/losses on metazoan phylogeny branches.
- Reconstructed ancestral species' genome content.
- Identified over/under-representation of functions and tissue specificity for gene dynamics.
Conclusions:
- MANTIS provides a crucial link between multi-species genome comparisons and functional analyses.
- The database supports in-depth investigation of gene evolution, phylogenetic mapping, and functional parameters.
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