LOCnet and LOCtarget: sub-cellular localization for structural genomics targets
1 CUBIC and 2 North East Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA, 3 Department of Physics, Columbia University, 538 West 120th Street, New York, NY 10027, USA and 4 Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, 1150 Saint Nicholas Avenue, New York, NY 10032, USA
* To whom correspondence should be addressed. Tel: +1 212 305 4018; Fax: +1 212 305 7932; Email: nair{at}maple.bioc.columbia.edu
Received February 15, 2004; Revised March 26, 2004; Accepted April 16, 2004
LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database for structural genomics, namely, TargetDB. LOCtarget predicts localization through a combination of four different methods: known nuclear localization signals (PredictNLS), homology-based transfer of experimental annotations (LOChom), inference through automatic text analysis of SWISS-PROT keywords (LOCkey) and de novo prediction through a system of neural networks (LOCnet). Additionally, we report predictions from SignalP. The final prediction is based on the method with the highest confidence. The web server can be used to predict sub-cellular localization of proteins from their amino acid sequence. The LOCtarget database currently contains localization predictions for all eukaryotic proteins from TargetDB and is updated every week. The server is available at http://www.rostlab.org/services/LOCtarget/.
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