InterPro protocols

View InterPro computational protocol

InterPro statistics

You need an account to access this content

info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Function prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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

Download


Versioning


Add your version

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 in pipelines

 (348)
2018
PMCID: 5765558
PMID: 29319806
DOI: 10.1093/gbe/evx271

[…] genome sequences were used to detect rrna genes by rnammer 1.2 (), and to detect trna and tmrna genes by aragorn 1.2.36 (). prodigal 2.6.2 () was applied to predict genes, and subsequently the interpro database 5.4-47.0 () was used to classify the genes and to predict domains and sites. at runtime, the following databases were selected: tigrfam, prodom, smart, prosite, pfama, prints, […]

2018
PMCID: 5776133
PMID: 29387078
DOI: 10.3389/fpls.2017.02272

[…] was performed using mega6 software (tamura et al., ). the putative motif and domains were analyzed with signalp 4.1 (http://www.cbs.dtu.dk/services/signalp/), interproscan (http://www.ebi.ac.uk/interpro/scan.html), and smart (http://smart.embl-heidelberg.de/). the sequences of the ssr markers that flank verticillium wilt-resistance quantitative trait loci (qtl) in cotton were downloaded […]

2018
PMCID: 5786227
PMID: 29329439
DOI: 10.1093/gbe/evy002

[…] ribonuclease iii homologs in r, irregulare described in the previous section. domain architectures were examined using smart 7 (http://smart.embl.de/) and interproscan v. 61.0 (https://www.ebi.ac.uk/interpro/) with each domain’s cut-off e-value = 1e−04. candidate containing both ribonuclease iii (riboc) domain (ipr000999) and double stranded rna-binding domain (dsrm) (ipr014720) were considered […]

2018
PMCID: 5802763
PMID: 29423235
DOI: 10.1038/s41438-017-0003-0

[…] databases were used for blast search and annotation. blast2go (v2.5.0) was used to obtain the go (http://geneontology.org) annotation, and interproscan5 (v5.11–51.0) was used to obtain the interpro (http://www.ebi.ac.uk/interpro) annotation. blast similarity searches were performed for pairwise comparisons of all four libraries (jj-vs-jhn, jj-vs-jh, jjd-vs-jhn, jjd-vs-jh, jhn-vs-jh, […]

2018
PMCID: 5804921
PMID: 29378020
DOI: 10.1093/gbe/evy011

[…] analyzed using the kaas server (). all programs were run with default values., the output of an interproscan of the translated protostelium aurantium transcripts was scanned for proteins harboring interpro domain ipr001054 for class iii adenylate and guanylate cyclases. the p. aurantium proteins harboring this domain were aligned with the five dictyostelium cyclases and a few signature ph. […]

InterPro in publications

 (3353)
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 […]

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 […]

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 […]

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; […]

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 […]

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.

InterPro reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review InterPro