PSORTdb is a database of protein

subcellular localization The cells of eukaryotic organisms are elaborately subdivided into functionally-distinct membrane-bound compartments. Some major constituents of eukaryotic cells are: extracellular space, plasma membrane, cytoplasm, nucleus, mitochondria, Golgi ap ...

(SCL) for

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

and

archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...

. It is a member of the PSORT family of

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

tools. The database consists of two datasets, ePSORTdb and cPSORTdb, which contain information determined through experimental validation and computational prediction, respectively. The ePSORTdb dataset is the largest curated collection of experimentally verified SCL data. PSORTdb was initially developed in 2005 in order to contain

protein subcellular localization prediction Protein subcellular localization prediction (or just protein localization prediction) involves the prediction of where a protein resides in a cell, its subcellular localization. In general, prediction tools take as input information about a protei ...

s for bacteria. The computational predictions in the cPSORTdb dataset were generated by the PSORT tool PSORTb 2.0, the most accurate SCL predictor of the time. The second and current version of PSORTdb was released in 2010. Entries in the database are automatically generated as newly sequenced prokaryotic genomes become available through

NCBI The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...

. As of the second release, ePSORTdb contained over 12,000 entries for bacterial proteins and 800 entries for archaeal proteins; cPSORTdb contained SCL predictions for over 3,700,000 proteins in total. The ePSORTdb data is derived from a manual literature search (using

PubMed PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintain the ...

) as well as

Swiss-Prot UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from ...

annotations. The cPSORTdb predictions are generated using the updated PSORTb 3.0 tool. PSORTdb can be accessed through a web interface or via

BLAST Blast or The Blast may refer to: * Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film) ...

. The entire database is also available for download under the

GNU General Public License The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the Four Freedoms (Free software), four freedoms to run, study, share, and modify the software. The license was th ...

. Each term in the database is associated with an identifier from the

Gene Ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and g ...

in order to allow integration with other bioinformatics resources. As of 2014, PSORTdb is maintained through the laboratory of Fiona Brinkman at

Simon Fraser University Simon Fraser University (SFU) is a public research university in British Columbia, Canada, with three campuses, all in Greater Vancouver: Burnaby (main campus), Surrey, and Vancouver. The main Burnaby campus on Burnaby Mountain, located from ...

.{{cite web, title=Computational Tools Developed - Fiona Brinkman Laboratory, url=http://www.brinkman.mbb.sfu.ca/computational-tools-developed/, accessdate=1 September 2014

References

External links

* http://db.psort.org/ Biological databases Protein targeting Post-translational modification

See also

References

External links