PSORTdb: a protein subcellular localization database for bacteria - PubMed (original) (raw)

PSORTdb: a protein subcellular localization database for bacteria

Sébastien Rey et al. Nucleic Acids Res. 2005.

Abstract

Information about bacterial subcellular localization (SCL) is important for protein function prediction and identification of suitable drug/vaccine/diagnostic targets. PSORTdb (http://db.psort.org/) is a web-accessible database of SCL for bacteria that contains both information determined through laboratory experimentation and computational predictions. The dataset of experimentally verified information (approximately 2000 proteins) was manually curated by us and represents the largest dataset of its kind. Earlier versions have been used for training SCL predictors, and its incorporation now into this new PSORTdb resource, with its associated additional annotation information and dataset version control, should aid researchers in future development of improved SCL predictors. The second component of this database contains computational analyses of proteins deduced from the most recent NCBI dataset of completely sequenced genomes. Analyses are currently calculated using PSORTb, the most precise automated SCL predictor for bacterial proteins. Both datasets can be accessed through the web using a very flexible text search engine, a data browser, or using BLAST, and the entire database or search results may be downloaded in various formats. Features such as GO ontologies and multiple accession numbers are incorporated to facilitate integration with other bioinformatics resources. PSORTdb is freely available under GNU General Public License.

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References

1. 1. Allan E. and Wren,B.W. (2003) Genes to genetic immunization: identification of bacterial vaccine candidates. Methods, 31, 193–198. - PubMed
2. 1. Mora M., Veggi,D., Santini,L., Pizza,M. and Rappuoli,R. (2003) Reverse vaccinology. Drug Discov. Today, 8, 459–464. - PubMed
3. 1. Paine K. and Flower,D.R. (2002) Bacterial bioinformatics: pathogenesis and the genome. J. Mol. Microbiol. Biotechnol., 4, 357–365. - PubMed
4. 1. Gardy J.L., Spencer,C., Wang,K., Ester,M., Tusnady,G.E., Simon,I., Hua,S., deFays,K., Lambert,C., Nakai,K. et al. (2003) PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res., 31, 3613–3617. - PMC - PubMed
5. 1. Boeckmann B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365–370. - PMC - PubMed

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