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Nucleic Acids Research, 2004, Vol. 32, Database issue D463-D467
© 2004 Oxford University Press

MitoProteome: mitochondrial protein sequence database and annotation system

Dawn Cotter1, Purnima Guda1, Eoin Fahy2 and Shankar Subramaniam*,1,3

1 San Diego Supercomputer Center, University of California, 9500 Gilman Drive, San Diego, CA 92037, USA, 2 MitoKor, 11494 Sorrento Valley Road, San Diego, CA 92121, USA and 3 Departments of Bioengineering, Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093-0612, USA

*To whom correspondence should be addressed at 9500 Gilman Drive, MC-0505 San Diego, CA 92093-0612, USA. Tel: +1 858 822 0986; Fax: +1 858 822 3752; Email: shankar{at}sdsc.edu

MitoProteome is an object-relational mitochondrial protein sequence database and annotation system. The initial release contains 847 human mitochondrial protein sequences, derived from public sequence databases and mass spectrometric analysis of highly purified human heart mitochondria. Each sequence is manually annotated with primary function, subfunction and subcellular location, and extensively annotated in an automated process with data extracted from external databases, including gene information from LocusLink and Ensembl; disease information from OMIM; protein–protein interaction data from MINT and DIP; functional domain information from Pfam; protein fingerprints from PRINTS; protein family and family-specific signatures from InterPro; structure data from PDB; mutation data from PMD; BLAST homology data from NCBI NR; and proteins found to be related based on LocusLink and SWISS-PROT references and sequence and taxonomy data. By highly automating the processes of maintaining the MitoProteome Protein List and extracting relevant data from external databases, we are able to present a dynamic database, updated frequently to reflect changes in public resources. The MitoProteome database is publicly available at http://www. mitoproteome.org/. Users may browse and search MitoProteome, and access a complete compilation of data relevant to each protein of interest, cross-linked to external databases.


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