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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

 (1373)
call_split

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

2018
Sci Rep
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5
call_split See protocol

[…] en 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 to determin […]

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

[…] S). 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 on B […]

library_books

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

2018
Sci Rep
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. […]

library_books

Molecular Characterization of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) Gene Family in Betula luminifera

2018
Front Plant Sci
PMCID: 5945835
PMID: 29780401
DOI: 10.3389/fpls.2018.00608

[…] the genome-specific gene-finding parameters of A. thaliana and P. trichocarpa (Softberry, http://www.softberry.com/berry.phtml; Solovyev et al., ). All the nonredundant gene models were submitted to Interpro (http://www.ebi.ac.uk/interpro) to confirm the presence of the SBP domain. Based on the predicted models, all the BlSPL genes were cloned and sequenced, and the predicted gene models were the […]

library_books

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

2018
Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] 8.97.239/PRINTS/index.php), PANTHER (http://www.pantherdb.org/), COILS (https://embnet.vital-it.ch/software/COILS_form.html) and MobiDB-lite (http://protein.bio.unipd.it/mobidblite/) accessed through InterPro version 64.0 (https://www.ebi.ac.uk/interpro/) using InterProScan 5,. In addition, the secreted proteins in Aspergillus species were annotated with GO terms using FungiFun2 (https://elbe.hki- […]

library_books

De Novo DNA Synthesis in Aedes aegypti Midgut Cells as a Complementary Strategy to Limit Dengue Viral Replication

2018
Front Microbiol
PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] ions (Guindon et al., ; Lefort et al., ), the protein tree was visualized and optimized using FigTree tool v1.4.3.Sequences obtained and aligned were subjected to Blast2GO for Gene Ontology Terms and Interpro domains features. […]

Citations

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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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