New developments in the InterPro database

By Nicola J. Mulder, Rolf Apweiler, T. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Virginie Buillard, L. Cerutti, Richard R. Copley and 35 more. Nucleic Acids Res., 2007

542 citations recorded by the source corpus.

InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (), and for download by anonymous FTP (). The InterProScan search tool is now also available via a web service at .

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. (2008, methodology): “Bioinformatic Protein Analysis We used InterProScan for domain/motif analyses (Mulder et al., 2007) and Mitoprot and ChloroP for the prediction of mitochondrial and chloroplast targeting sequences, respectively (Claros and Vincens, 1996; Emanuelsson et al.”
Genome Structure of the Legume, Lotus japonicus (2008, methodology): “For the analysis of gene families and functional domains, the predicted proteome was searched against InterPro.(39) InterPro annotations were assigned to each functional motif and domain, and then the annotation information was translated into GO functional descriptions.”
ToxoDB: an integrated Toxoplasma gondii database resource (2007, background): “[signal peptides, transmembrane domains, hydrophobicity plots, AA content and InterPro domains (9)], Gene Ontology function predictions, and BLAST similarities to the NCBI non-redundant protein database (Table 1).”
InterPro: the integrative protein signature database (2008, background): “No new member databases have been added to InterPro since the previous publication (1), but signatures from all the existing member databases continue to be integrated into new and existing InterPro entries.”
The yak genome and adaptation to life at high altitude (2012, methodology): “For yak reference genes, motifs and domains were determined by searches in InterProScan 55 of the sequences against publicly available databases, including Pfam, PRINTS, PROSITE, ProDom and SMART.”
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database (2008, methodology): “Using the standard conﬁguration ﬁle (log4j.properties) the logging can be directed to a ﬁle.”
High-throughput functional annotation and data mining with the Blast2GO suite (2008, background): “> threshold Additionally, Blast2GO provides the possibility to transfer GO terms obtained through protein domain information by InterProScan (18).”
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling (2010, background): “com/), Interpro (4), reactome (5)], regulatory information [Transfac (6), Jaspar (7), ORegAnno (8), miRNA target genes from miRBase (35)], protein–protein interactions (9) and text-mining module definitions (10).”
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny (2008, methodology): “The InterPro consortium integrates databases of protein families, domains and functional sites, including: Gene3D (30), PANTHER (31), Pfam (32), PIRSF (33), PRINTS (34), ProDom (35), PROSITE (36), SMART (37), SUPERFAMILY and TIGRFAMs (38).”
SMART 6: recent updates and new developments (2008, methodology): “In addition to SMART domains, we now also display the basic annotation for all detected Pfam (14) domains, such as Interpro (15) abstract and annotated Gene Ontology (16) terms.”
A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety (2007, methodology): “…were the base for gene annotations GO terms were extracted from BLAST searches against KEGG databases, KOBAS of metabolic pathways and InterproScan [118] and clustered using their semantic similarity [119], accuracy weight and the path from the root node of the ontology to the most detailed…”
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction (2009, methodology): “Given a protein sequence, the tool scans against various pattern and signature data sources collected by the InterPro project [53].”
DBD––taxonomically broad transcription factor predictions: new content and functionality (2007, methodology): “The DBD database has been used as an annotation tool in the context of the InterPro (8) and FlyTF (http://FlyTF.”
FlyBase: enhancing Drosophila Gene Ontology annotations (2008, methodology): “We have recently standardized our ‘inferred from electronic annotation’ (IEA) data such that it is based on a single source: a mapping between InterPro protein domains and GO terms (6).”
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks (2008, background): “Protein sequence pages (associated with a Gene page) are, in turn, additionally linked to records from GenPept (14), InterPro (37), PRINTS (38), PROSITE (39), ProDom (40), SMART (41), Pfam (42) and, when appropriate, to a species-specific gene page in FlyBase (43) or ZFIN (44).”