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Nucleic Acids Research 2006 34(Database Issue):D692-D696; doi:10.1093/nar/gkj055
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Nucleic Acids Research, 2006, Vol. 34, Database issue D692-D696
© 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

ChloroplastDB: the Chloroplast Genome Database

Liying Cui, Narayanan Veeraraghavan1, Alexander Richter1, Kerr Wall, Robert K. Jansen2, Jim Leebens-Mack, Izabela Makalowska1 and Claude W. dePamphilis*

Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University University Park, PA 16802, USA 1Center for Computational Genomics, Huck Institutes of Life Sciences, The Pennsylvania State University University Park, PA 16802, USA 2Section of Integrative Biology, The University of Texas at Austin Austin, TX 78712, USA

*To whom correspondence should be addressed. Tel: +1 814 863 6412; Fax: +1 814 865 9131; Email: cwd3{at}psu.edu

Received August 19, 2005. Revised October 4, 2005. Accepted October 4, 2005.

The Chloroplast Genome Database (ChloroplastDB) is an interactive, web-based database for fully sequenced plastid genomes, containing genomic, protein, DNA and RNA sequences, gene locations, RNA-editing sites, putative protein families and alignments (http://chloroplast.cbio.psu.edu/). With recent technical advances, the rate of generating new organelle genomes has increased dramatically. However, the established ontology for chloroplast genes and gene features has not been uniformly applied to all chloroplast genomes available in the sequence databases. For example, annotations for some published genome sequences have not evolved with gene naming conventions. ChloroplastDB provides unified annotations, gene name search, BLAST and download functions for chloroplast encoded genes and genomic sequences. A user can retrieve all orthologous sequences with one search regardless of gene names in GenBank. This feature alone greatly facilitates comparative research on sequence evolution including changes in gene content, codon usage, gene structure and post-transcriptional modifications such as RNA editing. Orthologous protein sets are classified by TribeMCL and each set is assigned a standard gene name. Over the next few years, as the number of sequenced chloroplast genomes increases rapidly, the tools available in ChloroplastDB will allow researchers to easily identify and compile target data for comparative analysis of chloroplast genes and genomes.


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