SAWTED: Structure Assignment With Text Description—Enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons

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Abstract
Motivation: Sequence database search methods often identify putative sub-threshold hits of known function or structure for a given query sequence. It is widespread practice to filter these hits by hand using knowledge of function and other factors; to the expert, some hits may appear more sensible than others. SAWTED (Structure Assignment With Text Description) is an automated solution to this post-filtering problem which will be applicable to large scale genome assignments. Results: A standard document comparison algorithm is applied to text descriptions extracted from SWISS-PROT annotations. The added value of SAWTED in combination with PSI-BLAST has been shown with a benchmark of difficult remote homologues taken from the SCOP structure database. Availability: A SAWTED PSI-BLAST Web server is available to perform sensitive searches against the protein structure database (http://www.bmm.icnet.uk/servers/sawted). Contact: R.MacCallum@icrf.icnet.uk

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