2002 InferringSCLThroughAutoLexAnalysis

• (Nair & Rost, 2002) ⇒ Rajesh Nair, Burkhard Rost. (2002). “Inferring Sub-cellular Localization Through Automated Lexical Analysis." Bioinformatics, 18(90001) doi:10.1093/bioinformatics/18.suppl_1.S78

Subject Headings: Protein Localization Information Extraction Task.

Cited By

• ~77 http://scholar.google.com/scholar?q=%22Inferring+sub-cellular+localization+through+automated+lexical+analysis.+2002

Quotes

Abstract

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

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	Author	volume	Date Value	title	type	journal	titleUrl	doi	note	year
2002 InferringSCLThroughAutoLexAnalysis	Rajesh Nair Burkhard Rost			Inferring Sub-cellular Localization Through Automated Lexical Analysis		Bioinformatics Subject Area	http://cubic.bioc.columbia.edu/papers/2002 loci text/paper.pdf			2002