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Nucleic Acids Research, 2004, Vol. 32, Database issue D148-D152
© 2004 Oxford University Press

EyeSite: a semi-automated database of protein families in the eye

David A. Lee*,1,2, Sandrine Fefeu1, Adrian A. Edo-Ukeh1,2, Christine A. Orengo2 and Christine Slingsby1

1 Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK and 2 Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK

*To whom correspondence should be addressed. Tel: +44 20 7679 3890; Fax: +44 20 7679 7193; Email: dlee{at}biochem.ucl.ac.uk

The EyeSite is a web-based database of protein families for proteins that function in the eye and their homologous sequences. The resource clusters proteins at different levels of homology in order to faciltate functional annotation of sequences and modelling of proteins from structural homologues. Eye proteins are organized into the tissue types in which they function and are clustered into homologous families using a novel protocol employing the TribeMCL algorithm. Homologous families are further subdivided into sequence clusters for which multiple sequence alignments are generated. Structural annotations from the CATH domain database are provided for nearly 90% of the sequences, and protein family annotations from the Pfam database for ~86%. Homology models have also been generated where appropriate. The EyeSite is stored in a relational database and is extensively linked to other online bioinformatics resources to help relate allelic variants, annotations and clinical details to the derived data in the database. The EyeSite is available for online search, sequence information and model retrieval at http://eyesite.cryst.bbk.ac.uk/.


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