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Nucleic Acids Research 2005 33(Database Issue):D605-D610; doi:10.1093/nar/gki048
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Nucleic Acids Research, 2005, Vol. 33, Database issue D605-D610
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

AMPDB: the Arabidopsis Mitochondrial Protein Database

Joshua L. Heazlewood and A. Harvey Millar*

Plant Molecular Biology Group, School of Biomedical and Chemical Sciences, The University of Western Australia, Crawley 6009, WA, Australia

* To whom correspondence should be addressed. Tel: +61 8 6648 7245; Fax: +61 8 6648 1148; Email: hmillar{at}cyllene.uwa.edu.au

Received August 12, 2004; Revised and Accepted September 30, 2004

The Arabidopsis Mitochondrial Protein Database is an Internet-accessible relational database containing information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana (http://www.ampdb.bcs.uwa.edu.au/). The database was formed using the total non-redundant nuclear and organelle encoded sets of protein sequences and allows relational searching of published proteomic analyses of Arabidopsis mitochondrial samples, a set of predictions from six independent subcellular-targeting prediction programs, and orthology predictions based on pairwise comparison of the Arabidopsis protein set with known yeast and human mitochondrial proteins and with the proteome of Rickettsia. A variety of precomputed physical–biochemical parameters are also searchable as well as a more detailed breakdown of mass spectral data produced from our proteomic analysis of Arabidopsis mitochondria. It contains hyperlinks to other Arabidopsis genomic resources (MIPS, TIGR and TAIR), which provide rapid access to changing gene models as well as hyperlinks to T-DNA insertion resources, Massively Parallel Signature Sequencing (MPSS) and Genome Tiling Array data and a variety of other Arabidopsis online resources. It also incorporates basic analysis tools built into the query structure such as a BLAST facility and tools for protein sequence alignments for convenient analysis of queried results.

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