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PSORTdb: a protein subcellular localization database for bacteria.

Sébastien Rey1, Michael Acab, Jennifer L Gardy

  • 1Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6.

Nucleic Acids Research
|December 21, 2004
PubMed
Summary
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PSORTdb is a comprehensive bacterial subcellular localization database, integrating experimental and computational data for protein function prediction and target identification. This resource aids researchers in developing improved prediction tools and understanding bacterial protein localization.

Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • Bacterial subcellular localization (SCL) is crucial for predicting protein function and identifying drug, vaccine, and diagnostic targets.
  • Existing resources may lack comprehensive, curated data for SCL.

Purpose of the Study:

  • To present PSORTdb, a web-accessible database of bacterial SCL.
  • To provide a manually curated dataset of experimentally verified SCL information.
  • To integrate computational predictions of SCL for proteins from complete bacterial genomes.

Main Methods:

  • Manual curation of approximately 2000 experimentally verified SCL proteins.
  • Computational analysis of proteins using the PSORTb predictor on NCBI sequenced genomes.
  • Development of a flexible web interface for data access (text search, browser, BLAST).

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Main Results:

  • PSORTdb offers the largest manually curated dataset of experimentally verified bacterial SCL.
  • The database includes computational SCL predictions for proteins from completely sequenced bacterial genomes.
  • Integrated features like GO ontologies and multiple accession numbers facilitate data integration.

Conclusions:

  • PSORTdb serves as a valuable resource for bacterial SCL research.
  • The database supports the development of improved SCL prediction tools.
  • PSORTdb facilitates integration with other bioinformatics resources for broader research applications.