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Protocols

InterPro specifications

Information


Unique identifier OMICS_01694
Name InterPro
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
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 http://www.ebi.ac.uk/interpro/training.html

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


No version available

Documentation


Maintainer


This tool is not maintained anymore.

Additional information


https://github.com/ebi-pf-team/interproscan/wiki http://www.ebi.ac.uk/interpro/training.html

Publications for InterPro

InterPro citations

 (3419)
library_books

Genomic and functional characterisation of IncX3 plasmids encoding blaSHV 12 in Escherichia coli from human and animal origin

2018
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5

[…] reading frames (orfs) were identified by rast version 2.0 and manually curated when necessary. blastp analyses of the putative orfs against the ncbi non-redundant proteins (nr) database, pfam, and interpro scan were used to assess their putative functions by identification of structural features and motifs,. resfinder (version 2.1), plasmidfinder (version 1.3) and isfinder were used […]

library_books

Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

2018
PMCID: 5952850
PMID: 29785177
DOI: 10.1186/s41065-018-0060-x

[…] the function of unigene sequences using no redundant (nr) protein database (ncbi), swiss prot database, kegg (kyoto encyclopedia of genes and genomes), cog (clusters of orthologous groups) and interpro database with an e-value<10− 5. blast2go software was used for gene ontology (go) annotation., the equivalent mixed rna samples (young leaves, stems and roots) from three individuals […]

call_split

Characterisation of proteins in excretory/secretory products collected from salmon lice, Lepeophtheirus salmonis

2018
PMCID: 5948691
PMID: 29751843
DOI: 10.1186/s13071-018-2885-6
call_split See protocol

[…] identified proteins were investigated using the blast2go software suite []. sequences were blasted against the ncbinr database. proteins were then assigned into functional groups by searching the interpro databases and gene ontology databases. annotations from both searches were then merged. the gene ontology (go) terms assigned to each protein were then used to construct pie charts based […]

library_books

First comprehensive analysis of lysine acetylation in Alvinocaris longirostris from the deep sea hydrothermal vents

2018
PMCID: 5946511
PMID: 29747590
DOI: 10.1186/s12864-018-4745-3

[…] (go) annotation proteome was derived from the uniprot-goa database (http://www.ebi.ac.uk/goa/). if the proteins were not annotated by uniprot-goa database, the interproscan (https://www.ebi.ac.uk/interpro) would be applied to annotate by protein sequence alignment method, which was also used for protein domain functional description. then proteins were then classified by go annotation […]

library_books

Identification of genes regulating ovary differentiation after pollination in hazel by comparative transcriptome analysis

2018
PMCID: 5941469
PMID: 29739322
DOI: 10.1186/s12870-018-1296-3

[…] unigenes to nt, nr, cog, kegg and swissprot to obtain annotations, blast2go (version: v2.5.0; parameters: default) [] with nr annotation to obtain go annotations, and interproscan5 [] to obtain interpro annotations. clean reads were mapped to unigenes using bowtie2 (version: v2.1.0) [] with options “q; phred64; sensitive; dpad, 0; gbar, 99999999; mp, 1, 1; np, 1; score-min l, 0, -0.1; i, 1; […]

library_books

Systematic analysis of DEMETER like DNA glycosylase genes shows lineage specific Smi miR7972 involved in SmDML1 regulation in Salvia miltiorrhiza

2018
PMCID: 5940787
PMID: 29739980
DOI: 10.1038/s41598-018-25315-w

[…] genes identified from other plants using the blastx algorithm (www.ncbi.nlm.nih.gov/blast/) and by alignment with rna-seq data of s. miltiorrhiza transcriptome (http://www.ncbi.nlm.nih.gov/sra). the interpro database (http://www.ebi.ac.uk/interpro/) was finally used to confirm each predicted protein sequence to be a dml., gene structures of smdmls, atdmls and osdmls were determined on the gene […]


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InterPro institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK; School of Computer Science, The University of Manchester, Manchester, UK; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, CA, USA; European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland; Medical Research Council Laboratory of Molecular Biology, Cambridge, UK; J. Craig Venter Institute (JCVI), Rockville, MD, USA; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA; Biobyte Solutions GmbH, Heidelberg, Germany; National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA; Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA; Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA; Department of Biomedical Sciences, University of Padua, Padua, Italy; Department of Agricultural Sciences, University of Udine, Udine, Italy; Fondazione Edmund Mach, S. Michele all’Adige, Italy; Structural and Molecular Biology, University College London, London, UK
InterPro funding source(s)
Supported by Wellcome Trust [108433/Z/15/Z]; Biotechnology and Biological Sciences Research Council [BB/N00521X/1, BB/N019172/1, BB/L024136/1]; National Science Foundation, Division of Biological Infrastructure [1458808]; Intramural Research Program of the National Library of Medicine at National Institutes of Health/DHHS; ELIXIR, the research infrastructure for life-science data; and the European Molecular Biology Laboratory core funds.

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