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Bioinformatics Vol. 18 no. 90001 2002
Pages S78-S86
© 2002 Oxford University Press

Inferring sub-cellular localization through automated lexical analysis

Rajesh Nair 1,2 and Burkhard Rost 1,3,*

1 CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
2 Department of Physics, Columbia University, 538 West 120th Street, New York, NY 10027, USA
3 Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, 1150 St. Nicholas Avenue, New York, NY 10032, USA

Received on January 24, 2002 ; revised on March 29, 2002 ; accepted on March 29, 2002

Motivation: The SWISS-PROT sequence database contains keywords of functional annotations for many proteins. In contrast, information about the sub-cellular localization is available for only a few proteins. Experts can often infer localization from keywords describing protein function. We developed LOCkey, a fully automated method for lexical analysis of SWISS-PROT keywords that assigns sub-cellular localization. With the rapid growth in sequence data, the biochemical characterisation of sequences has been falling behind. Our method may be a useful tool for supplementing functional information already automatically available.

Results: The method reached a level of more than 82% accuracy in a full cross-validation test. Due to a lack of functional annotations, we could infer localization for fewer than half of all proteins in SWISS-PROT. We applied LOCkey to annotate five entirely sequenced proteomes, namely Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (worm), Drosophila melanogaster (fly), Arabidopsis thaliana (plant) and a subset of all human proteins. LOCkey found about 8000 new annotations of sub-cellular localization for these eukaryotes.

Availability: Annotations of localization for eukaryotes at: http://cubic.bioc.columbia.edu/services/LOCkey

Contact: nair{at}cubic.bioc.coplumbia.edu rost{at}columbia.edu

Keywords: genome sequence analysis; predicting sub-cellular localization; protein function; lexical analysis.

* To whom correspondence should be addressed.


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