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LOCATE: a mammalian protein subcellular localization database.

Sprenger J, Lynn Fink J, Karunaratne S, Hanson K, Hamilton NA, Teasdale RD - Nucleic Acids Res. (2007)

Bottom Line: Over the past 2 years, the data in LOCATE have grown substantially.Other additions include computational subcellular localization predictions, automated computational classification of experimental localization image data, prediction of protein sorting signals and third party submission of literature data.Collectively, this database provides localization proteome for individual subcellular compartments that will underpin future systematic investigations of these regions.

View Article: PubMed Central - PubMed

Affiliation: ARC Centre of Excellence in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.

ABSTRACT
LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of mouse and human proteins. Over the past 2 years, the data in LOCATE have grown substantially. The database now contains high-quality localization data for 20% of the mouse proteome and general localization annotation for nearly 36% of the mouse proteome. The proteome annotated in LOCATE is from the RIKEN FANTOM Consortium Isoform Protein Sequence sets which contains 58 128 mouse and 64 637 human protein isoforms. Other additions include computational subcellular localization predictions, automated computational classification of experimental localization image data, prediction of protein sorting signals and third party submission of literature data. Collectively, this database provides localization proteome for individual subcellular compartments that will underpin future systematic investigations of these regions. It is available at http://locate.imb.uq.edu.au/

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Transmembrane topology and predicted motifs and domains display.
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Figure 1: Transmembrane topology and predicted motifs and domains display.

Mentions: The membrane organization of a protein is displayed relative to the other protein domains, using the DomainDraw macromolecular feature drawing program (12). These protein schematic diagrams include Pfam (v21.0) and SCOP (v1.69) predicted domains and subcellular sorting signals based on experimentally defined motifs (Figure 1). The complement of proteins with the individual protein features can be visualized (http://locate.imb.uq.edu.au/list_motifs.shtml).Figure 1.


LOCATE: a mammalian protein subcellular localization database.

Sprenger J, Lynn Fink J, Karunaratne S, Hanson K, Hamilton NA, Teasdale RD - Nucleic Acids Res. (2007)

Transmembrane topology and predicted motifs and domains display.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238969&req=5

Figure 1: Transmembrane topology and predicted motifs and domains display.
Mentions: The membrane organization of a protein is displayed relative to the other protein domains, using the DomainDraw macromolecular feature drawing program (12). These protein schematic diagrams include Pfam (v21.0) and SCOP (v1.69) predicted domains and subcellular sorting signals based on experimentally defined motifs (Figure 1). The complement of proteins with the individual protein features can be visualized (http://locate.imb.uq.edu.au/list_motifs.shtml).Figure 1.

Bottom Line: Over the past 2 years, the data in LOCATE have grown substantially.Other additions include computational subcellular localization predictions, automated computational classification of experimental localization image data, prediction of protein sorting signals and third party submission of literature data.Collectively, this database provides localization proteome for individual subcellular compartments that will underpin future systematic investigations of these regions.

View Article: PubMed Central - PubMed

Affiliation: ARC Centre of Excellence in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.

ABSTRACT
LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of mouse and human proteins. Over the past 2 years, the data in LOCATE have grown substantially. The database now contains high-quality localization data for 20% of the mouse proteome and general localization annotation for nearly 36% of the mouse proteome. The proteome annotated in LOCATE is from the RIKEN FANTOM Consortium Isoform Protein Sequence sets which contains 58 128 mouse and 64 637 human protein isoforms. Other additions include computational subcellular localization predictions, automated computational classification of experimental localization image data, prediction of protein sorting signals and third party submission of literature data. Collectively, this database provides localization proteome for individual subcellular compartments that will underpin future systematic investigations of these regions. It is available at http://locate.imb.uq.edu.au/

Show MeSH