Orthology prediction at scalable resolution by phylogenetic tree analysis |
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Authors: | René TJM van der Heijden Berend Snel Vera van Noort Martijn A Huynen |
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Institution: | (1) Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands |
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Abstract: | Background Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either
orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive
nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack
semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract
orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do
they document the relations between the orthologous groups. |
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Keywords: | |
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