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Bioinformatics Advance Access published online on June 15, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl286
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© 2006 The Author(s)
Received March 1, 2006
Accepted April 30, 2006

Applications note

Roundup: a multi-genome repository of orthologs and evolutionary distances

Todd F. DeLuca 1, I-Hsien Wu 1, Jian Pu 1, Thomas Monaghan 1, Leon Peshkin 1, Saurav Singh 1, and Dennis P. Wall 1 *

1 The Center for Biomedical Informatics & Department of Systems Biology, Harvard Medical School, Boston, MA 02115

* To whom correspondence should be addressed.
Dennis P. Wall, E-mail: dpwall{at}hms.harvard.edu


  Abstract

Summary: We have created a tool for ortholog and phylogenetic profile retrieval called Roundup. Roundup is backed by a massive repository of orthologs and associated evolutionary distances that was built using the reciprocal smallest distance algorithm, an approach that has been shown to improve upon alternative approaches of ortholog detection such as reciprocal blast. Presently, the Roundup repository contains all possible pair-wise comparisons for over 250 genomes, including 32 Eukaryotes, more than doubling the coverage of any similar resource. The orthologs are accessible through an intuitive web interface that allows searches by genome or gene identifier, presenting results as phylogenetic profiles together with gene and molecular function annotations. Results may be downloaded as phylogenetic matrices for subsequent analysis, including the construction of whole-genome phylogenies based on gene-content data.

Availability: http://rodeo.med.harvard.edu/tools/roundup.

Associate Editor: Christos Ouzounis
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