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Nucleic Acids Research 2006 34(Database Issue):D363-D368; doi:10.1093/nar/gkj123
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Nucleic Acids Research, 2006, Vol. 34, Database issue D363-D368
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups

Feng Chen, Aaron J. Mackey, Christian J. Stoeckert, Jr and David S. Roos*

Departments of Chemistry, Biology and Genetics, Center for Bioinformatics, Penn Genomics Institute, University of Pennsylvania Philadelphia, PA 19104-6018, USA

*To whom correspondence should be addressed. Tel: +1 215 898 2118; Fax: +1 215 746 6697; Email: droos{at}sas.upenn.edu

Received August 15, 2005. Revised October 20, 2005. Accepted October 20, 2005.

The OrthoMCL database (http://orthomcl.cbil.upenn.edu) houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages, and most currently available complete eukaryotic genomes: 24 unikonts (12 animals, 9 fungi, microsporidium, Dictyostelium, Entamoeba), 4 plants/algae and 7 apicomplexan parasites. OrthoMCL software was used to cluster proteins based on sequence similarity, using an all-against-all BLAST search of each species' proteome, followed by normalization of inter-species differences, and Markov clustering. A total of 511 797 proteins (81.6% of the total dataset) were clustered into 70 388 ortholog groups. The ortholog database may be queried based on protein or group accession numbers, keyword descriptions or BLAST similarity. Ortholog groups exhibiting specific phyletic patterns may also be identified, using either a graphical interface or a text-based Phyletic Pattern Expression grammar. Information for ortholog groups includes the phyletic profile, the list of member proteins and a multiple sequence alignment, a statistical summary and graphical view of similarities, and a graphical representation of domain architecture. OrthoMCL software, the entire FASTA dataset employed and clustering results are available for download. OrthoMCL-DB provides a centralized warehouse for orthology prediction among multiple species, and will be updated and expanded as additional genome sequence data become available.


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