InterPro pipeline

InterPro specifications

Information


Unique identifier OMICS_01694
Name InterPro
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/InterPro

Documentation


Maintainer


  • person_outline Robert Finn <>

Additional information


https://github.com/ebi-pf-team/interproscan/wiki

Information


Unique identifier OMICS_01694
Name InterPro
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
Output format TSV, XML, JSON, GFF3, HTML, SVG
Operating system Unix/Linux
Programming languages C++, Java, Perl, Shell (Bash), Other
License Apache License version 2.0
Computer skills Advanced
Version 5.24-63.0
Stability Stable
Wikipedia https://en.wikipedia.org/wiki/InterPro

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Versioning


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Documentation


Maintainer


This tool is not maintained anymore.

Additional information


https://github.com/ebi-pf-team/interproscan/wiki

Publications for InterPro

InterPro IN pipelines

 (8)
2017
PMCID: 5598433
PMID: 28924494
DOI: 10.7717/peerj.3698

[…] to the categories r (general function prediction only) and s (function unknown) (fig. s1). with interproscan a predicted function could be assigned to 82% of the predicted proteins. based on the interpro and priam classifications (claudel-renard et al., 2003), an enzymatic function could be predicted for more than 500 proteins., analysis of the cds predicted from the r. ilealis cribt genome […]

2016
PMCID: 5217101
PMID: 27852011
DOI: 10.1534/g3.116.035923

[…] protein sequences corresponding to newly predicted coding genes were retrieved from the ncbi proteome (ftp://ftp.ncbi.nih.gov/genomes/gallus_gallus/protein/protein.fa.gz) and scanned for conserved interpro signatures in 11 databases of protein predictive models (mitchell et al. 2015) (file s1 and table s2). blast2go (gotz et al. 2008) suite (v3.2) was used to perform comprehensive gene […]

2014
PMCID: 4047054
PMID: 24901469
DOI: 10.1371/journal.pone.0099074

[…] an overlap in the expression domain., in this study, we identified flz family genes from 41 species of viridiplantae. using the key word ‘duf581’, a search was performed in pfam, plaza v 2.5 and interpro [3], [21], [19]. genes were also identified from phytozome using pfam identifier, pf04570 [20]. flz genes from solanaceae were identified from solanaceae genomic resource using interpro id […]

2014
PMCID: 4071342
PMID: 25018762
DOI: 10.3389/fpls.2014.00299

[…] additionally, 11 of the 12 proteins in this family contained three multicopper oxidase (mco) domains and the remaining protein (pgt_20719) contained two of the three domains (figure 7a). the interpro domains identified include: cupredoxin domain (ipr008972), multicopper oxidase, type 1 (ipr001117), and multicopper oxidase, type 2 (ipr011706), and multicopper oxidase, type 3 domain […]

2013
PMCID: 3616871
PMID: 23432914
DOI: 10.1186/1471-2164-14-123

[…] complexes, and reactions. first, orfs are inspected for the presence of different protein signatures (such as families, regions, domains, repeats, and sites) by using interproscan [89] and the interpro database [90]. these signatures are used for the classification and automatic annotation of protein sequences by assigning biological functions and gene ontology (go) terms. second, each orf […]

InterPro institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Faculty of Life Science and School of Computer Science, The University of Manchester, Manchester, UK; Swiss Institute of Bioinformatics (SIB), CMU, Geneva, Switzerland; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Department of Biochemistry, University of Geneva, Geneva, Switzerland; Pole Rhone-Alpin de Bio-Informatique (PRABI), Batiment G. Mendel, Universite Claude Bernard, Villeurbanne, France; European Molecular Laboratory (EMBL), Heidelberg, Germany; Department of Computer Science, University of Bristol, Bristol, UK; J. Craig Venter Institute (JCVI), Rockville, MD, USA; Protein Information Resource (PIR), Georgetown University Medical Center, Washington, DC, WA, USA; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA; Structural and Molecular Biology Department, University College London, University of London, London, UK; Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
InterPro funding source(s)
Supported by Biotechnology and Biological Sciences Research Council (BBSRC) [BB/L024136/1] and European Molecular Biology Laboratory (EMBL) core funds.

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