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The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences

Yeats, C; Lees, J; Carter, P; Sillitoe, I; Orengo, C; (2011) The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. Nucleic Acids Research , 39 W546-W550. 10.1093/nar/gkr438. Green open access

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Abstract

The Gene3D structural domain database provides domain annotations for 7 million proteins, based on the manually curated structural domain superfamilies in CATH. These annotations are integrated with functional, genomic and molecular information from external resources, such as GO, EC, UniProt and the NCBI Taxonomy database. We have constructed a set of web services that provide programmatic access to this integrated database, as well as the Gene3D domain recognition tool (Gene3DScan) and protein sequence annotation pipeline for analysing novel protein sequences. Example queries include retrieving all curated GO terms for a domain superfamily or all the multi-domain architectures for the human genome. The services can be accessed using simple HTTP calls and are able to return results in a range of formats for quick downloading and easy parsing, graphical rendering and data storage. Hence, they provide a simple, but flexible means of integrating domain annotations and associated data sets into locally run pipelines and analysis software. The services can be found at http://gene3d.biochem.ucl.ac.uk/WebServices/.

Type: Article
Title: The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/nar/gkr438
Publisher version: http://dx.doi.org/10.1093/nar/gkr438
Language: English
Additional information: This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: DATABASE, GENOMES, ARCHITECTURES, MODEL, CATH
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
URI: https://discovery.ucl.ac.uk/id/eprint/1396625
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