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Nucleic Acids Research, 2003, Vol. 31, No. 1 334-341
© 2003 Oxford University Press

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification

Paul D. Thomas*, Anish Kejariwal, Michael J. Campbell, Huaiyu Mi, Karen Diemer, Nan Guo, Istvan Ladunga, Betty Ulitsky-Lazareva, Anushya Muruganujan, Steven Rabkin, Jody A. Vandergriff and Olivier Doremieux

Protein Informatics, Celera Genomics, 850 Lincoln Center Drive, Foster City, CA 94404, USA

*To whom correspondence should be addressed. Email: paul.thomas{at}fc.celera.com

ABSTRACT

The PANTHER database was designed for high-throughput analysis of protein sequences. One of the key features is a simplified ontology of protein function, which allows browsing of the database by biological functions. Biologist curators have associated the ontology terms with groups of protein sequences rather than individual sequences. Statistical models (Hidden Markov Models, or HMMs) are built from each of these groups. The advantage of this approach is that new sequences can be automatically classified as they become available. To ensure accurate functional classification, HMMs are constructed not only for families, but also for functionally distinct subfamilies. Multiple sequence alignments and phylogenetic trees, including curator-assigned information, are available for each family. The current version of the PANTHER database includes training sequences from all organisms in the GenBank non-redundant protein database, and the HMMs have been used to classify gene products across the entire genomes of human, and Drosophila melanogaster. PANTHER is publicly available on the web at http://panther.celera.com.


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