Published online 20 November 2014 Nucleic Acids Research, 2015, Vol. 43, Database issue D227–D233 doi: 10.1093/nar/gku1041 The SUPERFAMILY 1.75 database in 2014: a doubling of data Matt E. Oates1,*, Jonathan Stahlhacke1, Dimitrios V. Vavoulis1, Ben Smithers1, Owen J.L. Rackham1,2, Adam J. Sardar1,3, Jan Zaucha1,4, Natalie Thurlby1,4, Hai Fang1 and Julian Gough1
1Computer Science, University of Bristol, Bristol, BS8 1UB, UK, 2Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK, 3e-Therapeutics plc,17 Blenheim Office Park, Long Hanborough, Oxfordshire, OX29 8LN, UK and 4Bristol Centre for Complexity Sciences, University of Bristol, Bristol, UK
Received October 01, 2014; Revised October 10, 2014; Accepted October 10, 2014
ABSTRACT quence is the main focus of the resource, but over time ad- ditional annotations and features for functional and phylo- We present updates to the SUPERFAMILY 1.75 (http: genetic analysis have been introduced. The database is built //supfam.org) online resource and protein sequence around a library of 15 438 expert-curated hidden Markov collection. The hidden Markov model library that pro- models (HMM) representing all protein domains of known vides sequence homology to SCOP structural do- structure. The classification of these domains is taken from mains remains unchanged at version 1.75. In the last the Structural Classification of Protein (SCOP) database 4 years SUPERFAMILY has more than doubled its (2). SCOP classifies protein domains into a hierarchy ac- holding of curated complete proteomes over all cel- cording to similarity in structure, at increasing levels of lular life, from 1400 proteomes reported previously in similarity and evolutionary relationship including: Class, 2010 up to 3258 at present. Outside of the main se- Fold, Superfamily and Family levels. The SUPERFAMILY quence collection, SUPERFAMILY continues to pro- database focuses on the Superfamily level, but additionally provides protein domain assignments at the Family level (3). vide domain annotation for sequences provided by Two domains are strictly grouped into the same Superfam- other resources such as: UniProt, Ensembl, PDB, ily if there is structural evidence for a common ancestor (4). much of JGI Phytozome and selected subcollections In general, the Family level SCOP annotation has also been of NCBI RefSeq. Despite this growth in data volume, found to be functionally consistent (5), and has a closer evo- SUPERFAMILY now provides users with an expanded lutionary relationship often directly observable at the level and daily updated phylogenetic tree of life (sTOL). of amino acid sequence. For these reasons, inclusion of a This tree is built with genomic-scale domain anno- domain at both the Superfamily and Family level within a tation data as before, but constantly updated when species can be thought of as evolutionary characters. The new species are introduced to the sequence library. genomic inclusion of an individual domain annotation and Our Gene Ontology and other functional and phe- in combination with other domains is the basis of our daily notypic annotations previously reported have stood updated phylogenetic tree of life (6). The SUPERFAMILYwebsite offers a variety of methods up to critical assessment by the function prediction to analyse whole proteins and domains. A keyword search community. We have now introduced these data in an is available from all pages on the site, and sequences can integrated manner online at the level of an individual be directly annotated against the HMM library from the sequence, and––in the case of whole genomes––with ‘Sequence search’ page. At the genomic level the user can enrichment analysis against a taxonomically defined investigate under- and overrepresentation of domains (4), background. view phylogenetic trees (6), plot domain architectures and networks (7) and examine the distribution of domain su- perfamilies or families across the tree of life (8). The dcGO INTRODUCTION resource (9) has undergone continued development provid- SUPERFAMILY (1) is both a database and website re- ing improved ontological annotations for SUPERFAMILY source available freely to the public. Predicting the presence domains and their combinations, more on this is discussed of protein domains of known structure in amino acid se- below.
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