Inferring sub-cellular localization through automated lexical analysis

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.

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