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Database (Oxford). 2015 Feb 27;2015. pii: bav003. doi: 10.1093/database/bav003. Print 2015.

LocSigDB: a database of protein localization signals.

Author information

1
Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA.
2
Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA.
3
Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA babu.guda@unmc.edu.

Abstract

LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will help support many important areas of biomedical research. By performing an extensive literature study, we compiled a collection of 533 experimentally determined localization signals, along with the proteins that harbor such signals. Each signal in the LocSigDB is annotated with its localization, source, PubMed references and is linked to the proteins in UniProt database along with the organism information that contain the same amino acid pattern as the given signal. From LocSigDB webserver, users can download the whole database or browse/search for data using an intuitive query interface. To date, LocSigDB is the most comprehensive compendium of protein localization signals for eight distinct subcellular locations. Database URL: http://genome.unmc.edu/LocSigDB/.

PMID:
25725059
PMCID:
PMC4343182
DOI:
10.1093/database/bav003
[Indexed for MEDLINE]
Free PMC Article

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