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A comprehensive database of gene orthologs for over 1800 genomes, including eukaryota, bacteria, archaea and viruses. Orthologs are inferred using the reciprocal smallest distance algorithm. Roundup provides two ways to search for orthologs. First, the Browse query is a genome-centric search that retrieves all orthologs between one genome and a set of other genomes. Results can be filtered by gene name or gene identifier. The second query, retrieve, returns all orthologs for all pairs of genomes in a set of genomes the user specifies. Data include clusters of orthologs for a wide range of sequence conservation, allowing searches for distant orthologs, and also phylogenetic profiles that enable functional investigation, phylogenetic analysis and prediction of network organization.

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Roundup classification

Roundup specifications

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The Center for Biomedical Informatics, Harvard Medical School and Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA

Funding source(s)

National Science Foundation (0543480 and 0640809); the National Institutes of Health (LM009261).

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