Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database | Zendy

Daniel Buchan | Zendy; Adrian J. Shepherd | Zendy; Lee David | Zendy; Frances M. G. Pearl | Zendy; Stuart Rison | Zendy; Janet M. Thornton | Zendy; Christine Orengo | Zendy

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Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

Author(s) -

Daniel Buchan,

Adrian J. Shepherd,

Lee David,

Frances M. G. Pearl,

Stuart Rison,

Janet M. Thornton,

Christine Orengo

Publication year - 2002

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.213802

Subject(s) - biology , genome , gene , computational biology , gene annotation , annotation , sequence alignment , database , genetics , computer science , peptide sequence

We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies.

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