Bioinformatics Advance Access originally published online on June 15, 2006
Bioinformatics 2006 22(16):2044-2046; doi:10.1093/bioinformatics/btl286
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
Roundup: a multi-genome repository of orthologs and evolutionary distances
The Center for Biomedical Informatics & Department of Systems Biology, Harvard Medical School Boston, MA 02115, USA
*To whom correspondence should be addressed.
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Abstract |
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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
Contact: dpwall{at}hms.harvard.edu
Associate Editor: Christos Ouzounis
Received on March 1, 2006; accepted on April 30, 2006
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