Inferring sub-cellular localization through automated lexical analysis.
BACKGROUND
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.
Nair
Rajesh
R
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA. nair@cubic.bioc.coplumbia.edu
Rost
Burkhard
B
D000043:Abstracting and Indexing / Q000379:methods*; D000465:Algorithms; D000818:Animals; D022082:Cellular Structures / Q000378:metabolism*; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated; D011506:Proteins / Q000737:chemistry / Q000145:classification* / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods; D014018:Tissue Distribution; D018875:Vocabulary, Controlled
D011506:Proteins