Interpro download

Christian J. Paul D. Cathy H. Author information Article notes Copyright and License information Disclaimer. This article has been cited by other articles in PMC. Table 1. Open in a separate window. Web interface 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.

Figure 1. Conflict of interest statement. None declared. New developments in the InterPro database. The Pfam protein families database. The ProDom database of protein domain families: more emphasis on 3D. SMART 5: domains in the context of genomes and networks. PIRSF family classification system for protein functional and evolutionary analysis. Gene3D: comprehensive structural and functional annotation of genomes. UniProt Consortium. InterProScan: protein domains identifier. UniProt Archive.

PLoS Pathogens. Curated genome annotation of Oryza sativa ssp. Genome Res. The Gene Ontology GO database and informatics resource. The predictive power of the CluSTr database.

Nucleic Acid Res. InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data.

One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site.

InterPro release 8. InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in as a means of amalgamating the major protein signature databases into one comprehensive resource.

The results are provided in a single format that rationalises the results that would be obtained by searching the member databases individually.

The latest release of InterPro contains entries describing families, domains, 95 repeats and 15 post-translational modifications. New features of the database include improved searching capabilities and enhanced graphical user interfaces for visualisation of the data. The exponential increase in the submission of nucleotide sequences to the nucleotide sequence database by genome sequencing centres has resulted in a need for rapid, automatic methods for classification of the resulting protein sequences.

There are several signature and sequence cluster-based methods for protein classification, each resource having distinct areas of optimum application owing to the differences in the underlying analysis methods. In recognition of this, InterPro was developed as an integrated documentation resource for protein families, domains and functional sites, to rationalise the complementary efforts of the individual protein signature database projects.

Related signatures from each member database are unified into single InterPro entries. Each InterPro entry includes a unique accession number, functional descriptions and literature references, and links are made back to the relevant member database s. Release 4. The database is freely accessible for text- and sequence-based searches. It is a useful resource that aids the functional classification of proteins.

InterPro also gives insights into the domain composition of the classified proteins and has applications in the functional classification of newly determined sequences lacking biochemical characterization, and in comparative genome analysis.

A comparison of the actinopterygii protein sequences against the sequences of other eukaryotes confirms the high representation of eukaryotic protein kinase in the organisms studied. The comparisons also show that, based on InterPro families, the trans-species evolution of MHC class I and II molecules in mammals and teleost fish can be recognized. Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function.

Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database s. Release 2. Questions can be emailed to interhelp ebi.

Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database s , allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc. Merged and individual entries i. Reduce Operating Costs. Reduce Time to Action.

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When additional data needs to be captured, or a specific test needs be run, screens dynamically change to reflect those requirements. If more guidance is required, provide work aids such a schematics, blueprints and how-to videos. It provides a downloadable version of the InterProScan software as well as various files containing pre-calculated InterPro data for the current release that can be downloaded. Data from previous releases are available in the InterPro ftp. The export button, found on various entry pages in InterPro, is located next to the text filter at the top of result tables.

When the file to generate is too big bigger than 10K entities we recommend to use a script to get the information from the API. See Your downloads for more information on how to generate a script.