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Nucleic Acids Research 2006 34(Database Issue):D724-D730; doi:10.1093/nar/gkj045
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Nucleic Acids Research, 2006, Vol. 34, Database issue D724-D730
© 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

Phytome: a platform for plant comparative genomics

Stefanie Hartmann, Dihui Lu1, Jason Phillips and Todd J. Vision*

Department of Biology, University of North Carolina at Chapel Hill Chapel Hill, NC 27599, USA 1School of Information and Library Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC 27599, USA

*To whom correspondence should be addressed. Tel: +1 919 843 4507; Fax: +1 919 962 1625; Email: tjv{at}bio.unc.edu

Received August 15, 2005. Revised October 4, 2005. Accepted October 4, 2005.

Phytome is an online comparative genomics resource that can be applied to functional plant genomics, molecular breeding and evolutionary studies. It contains predicted protein sequences, protein family assignments, multiple sequence alignments, phylogenies and functional annotations for proteins from a large, phylogenetically diverse set of plant taxa. Phytome serves as a glue between disparate plant gene databases both by identifying the evolutionary relationships among orthologous and paralogous protein sequences from different species and by enabling cross-references between different versions of the same gene curated independently by different database groups. The web interface enables sophisticated queries on lineage-specific patterns of gene/protein family proliferation and loss. This rich dataset is serving as a platform for the unification of sequence-anchored comparative maps across taxonomic families of plants. The Phytome web interface can be accessed at the following URL: http://www.phytome.org. Batch homology searches and bulk downloads are available upon free registration.


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