InterPro in 2011: new developments in the family and domain prediction database

By S. Hunter, Philip Jones, Alex L. Mitchell, Rolf Apweiler, Terri K. Attwood, Alex Bateman, Thomas Bernard, David Binns, Peer Bork, Sarah W. Burge and 40 more. 2011

1,139 citations recorded by the source corpus.

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.

Subfields: Molecular Biology

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Citations in the corpus

UniProt: a hub for protein information (2014, methodology): “Both UniRules and SAAS use the hierarchical InterPro classification of protein family and domain signatures (15) as a basis for protein classification and functional annotation.”
InterProScan 5: genome-scale protein function classification (2014, methodology): “By default, InterProScan 5 uses a pure in-memory database, which requires no configuration.”
GeneMANIA Prediction Server 2013 Update (2013, background): “…BioGRID (24) for physical (i.e., protein) interactions and genetic interactions; Gene Expression Omnibus (GEO) for co-expression networks (25); InterPro, via Ensembl, for protein domains (26); I2D for networks of interologs of physical interactions (27); and from our own manual curation efforts.”
MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data (2012, methodology): “The results of these analysis tools are stored in specific relational tables within PkGDB (1), together with the primary data used as inputs [UniProt (7), InterPro (8), COG (9), etc.”
SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage (2013, methodology): “Currently, the Web-Service allows to fetch for a given sequence all instances in the primary databases, to lookup of precalculated Interpro hits and sequence features, and to retrieve of homology information in either the SIMAP internal XML schema or formatted as BLAST XML output.”
New and continuing developments at PROSITE (2012, methodology): “html), an integrated database of protein signatures used for the classification and annotation of proteins and genomes (5).”
The InterPro protein families database: the classification resource after 15 years (2014, background): “0 in 2012 (21)), with an additional 5081 signatures being integrated into 3993 new entries.”
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs (2012, methodology): “In addition, database cross-referencing of gene identifiers enhances search term matches through available gene names and synonyms, InterPro, or GO identifiers, as well as secondary identifiers from UniProt, Entrez GeneID, RefSeq, Protein Data Bank, OMIM, PubMed and model organism databases.”
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models (2014, methodology): “They are, for example, used in the annotation of both protein domains [6-9] and genomic sequence derived from ancient transposable element expansions [10].”
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics (2012, background): “For example, GO, KEGG pathways, structural information via the InterPro protein domains (22) and regulatory information from microRNAs targets from mirBase (23).”
Expanded microbial genome coverage and improved protein family annotation in the COG database (2014, methodology): “The existing COG annotations were verified by comparing them to the annotations of the COG members in UniProt and RefSeq databases (28,34), protein domain names in the Pfam, InterPro and CDD databases (3,7,12), and, for COGs that contained representatives of the respective model organisms, functiona”