title: EyeSite: a semi-automated database of protein families in the eye.
abstract: 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 facilitate 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 approximately 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/.
authors.affiliation: Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK. dlee@biochem.ucl.ac.uk
authors.forename: David A
authors.initials: DA
authors.lastname: Lee
authors.forename: Sandrine
authors.initials: S
authors.lastname: Fefeu
authors.forename: Adrian A
authors.initials: AA
authors.lastname: Edo-Ukeh
authors.forename: Christine A
authors.initials: CA
authors.lastname: Orengo
authors.forename: Christine
authors.initials: C
authors.lastname: Slingsby
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001331:Automation; D019295:Computational Biology; D030562:Databases, Protein; D005123:Eye / Q000378:metabolism*; D005136:Eye Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009928:Organ Specificity; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D040681:Structural Homology, Protein
chemical_list: D005136:Eye Proteins