Abstract
Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of globular domain annotations for millions of available protein sequences. Gene3D has previously featured in the Database issue of NAR and here we report a significant update to the Gene3D database. The current release, Gene3D v16, has significantly expanded its domain coverage over the previous version and now contains over 95 million domain assignments. We also report a new method for dealing with complex domain architectures that exist in Gene3D, arising from discontinuous domains. Amongst other updates, we have added visualization tools for exploring domain annotations in the context of other sequence features and in gene families. We also provide web-pages to visualize other domain families that co-occur with a given query domain family.
Highlights
Sequence and structural databases continue to expand rapidly, with the current version of UniProtKB (v2017 08) containing nearly 90 million sequences (1)
There are several important improvements in the current release of Gene3D v16 compared to the v14 published previously (3)
We have added to the website comparative genomics tools for displaying domains in gene trees and changes in domain family partners in proteins across different genomes
Summary
Sequence and structural databases continue to expand rapidly, with the current version of UniProtKB (v2017 08) containing nearly 90 million sequences (1). Gene3D uses profile-Hidden Markov Models built from the CATH domain sequences to predict structural domains for proteins. We have moved our domain assignments to the latest release of CATH (v4.2) and improved the HMM building process, providing greater coverage of sequence space. We have added to the website comparative genomics tools for displaying domains in gene trees and changes in domain family partners in proteins across different genomes.
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