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BMCBI
2002

RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs

9 years 7 months ago
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
Background: When analyzing protein sequences using sequence similarity searches, orthologous sequences (that diverged by speciation) are more reliable predictors of a new protein's function than paralogous sequences (that diverged by gene duplication). The utility of phylogenetic information in high-throughput genome annotation ("phylogenomics") is widely recognized, but existing approaches are either manual or not explicitly based on phylogenetic trees. Results: Here we present RIO (Resampled Inference of Orthologs), a procedure for automated phylogenomics using explicit phylogenetic inference. RIO analyses are performed over bootstrap resampled phylogenetic trees to estimate the reliability of orthology assignments. We also introduce supplementary concepts that are helpful for functional inference. RIO has been implemented as Perl pipeline connecting several C and Java programs. It is available at [http:// www.genetics.wustl.edu/eddy/forester/] . A web server is at [h...
Christian M. Zmasek, Sean R. Eddy
Added 17 Dec 2010
Updated 17 Dec 2010
Type Journal
Year 2002
Where BMCBI
Authors Christian M. Zmasek, Sean R. Eddy
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