InterProScan protocols

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InterProScan specifications


Unique identifier OMICS_01479
Name InterProScan
Alternative names InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A file containing unaligned sequences.
Input format FASTA
Output data Results for protein and nucleotide sequences.
Operating system Unix/Linux
Programming languages C++, Java, Perl, Shell (Bash)
License Apache License version 2.0
Computer skills Advanced
Version 5.26-65.0
Stability Stable
Maintained Yes



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  • person_outline Alex Mitchell <>
  • person_outline Team InterProScan <>

Additional information


Unique identifier OMICS_01479
Name InterProScan
Alternative names InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5
Interface Web user interface, Application programming interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained No



This tool is not maintained anymore.

Additional information

Publications for InterProScan

InterProScan in pipelines

PMCID: 5766596
PMID: 29330436
DOI: 10.1038/s41598-017-18534-0

[…] kegg (, and swissprot ( we generated gene ontology (go) annotations for our unigenes with blast2go v2.5.0, and used interproscan5 v5.11–51.0 to generate interpro ( annotations., we selected the segment of each unigene that best mapped to one or more functional databases as its coding […]

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

[…] phylogenetic analysis was performed using mega6 software (tamura et al., ). the putative motif and domains were analyzed with signalp 4.1 (, interproscan (, and smart ( the sequences of the ssr markers that flank verticillium wilt-resistance quantitative trait loci […]

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

[…] 3) were found during the identification of ribonuclease iii homologs in r, irregulare described in the previous section. domain architectures were examined using smart 7 ( and interproscan v. 61.0 ( with each domain’s cut-off e-value = 1e−04. candidate containing both ribonuclease iii (riboc) domain (ipr000999) and double stranded […]

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

[…] swiss-prot ( databases were used for blast search and annotation. blast2go (v2.5.0) was used to obtain the go ( annotation, and interproscan5 (v5.11–51.0) was used to obtain the interpro ( annotation. blast similarity searches were performed for pairwise comparisons of all four libraries […]

PMCID: 5805871
PMID: 29439033
DOI: 10.1128/genomeA.00022-18

[…] the ezbiocloud database, which showed that strain k27 is most similar to s. marcescens subsp. sakuensis kctc 42172 (clg_48654), with a probability of 100% (). protein functions were predicted using interproscan5 (), while the presence of a secondary metabolite biosynthesis gene cluster in the genome was identified by antismash ()., to date, no study has reported on the genome sequence […]

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InterProScan in publications

PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] (, employing tools of augustus (), genemark.hmm-es (), and evm (). gene function was inferred from matches to the databases of pfam (), merops (), cazy (), interproscan (), and swiss-prot (). product descriptions were assigned with homologues with 60% similarity across 60% of the protein length (). cegma v2.4.010312 was used to identify the presence […]

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

[…] functional annotation. gene ontology (go) annotation proteome was derived from the uniprot-goa database ( if the proteins were not annotated by uniprot-goa database, the interproscan ( would be applied to annotate by protein sequence alignment method, which was also used for protein domain functional description. then proteins […]

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

[…] we used blast [] to align 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; […]

PMCID: 5945886
PMID: 29780372
DOI: 10.3389/fmicb.2018.00861

[…] against the laccase and multicopper oxidase engineering database (lcced) (e-value < 10-8, identity ≥ 20%, and query length coverage ≥ 20%) (). the protein signatures were detected using the interproscan web service ()., contig taxonomic assignment was carried out using megan v5.10.6 (), based on blastx analysis against the non-redundant ncbi database (min. score = 35, min. support = 1). […]

PMCID: 5935921
PMID: 29728068
DOI: 10.1186/s12864-018-4691-0

[…] p. tricornutum and t. pseudonana were performed. the query sequences were collected from the kegg pathway. hits with e-value < 10− 5 were then checked for sequence domain and motif content using interproscan [], to verify that they contained the relevant domains as the targeted protein. finally, phylogenetic trees of the sequences with the relevant domains and the query were drawn […]

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InterProScan institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
InterProScan funding source(s)
Supported by Biotechnology and Biological Sciences Research Council (Bioinformatics and Biological Resources Fund) (BB/ F010508/1); European Union (under the program ‘FP7 capacities: Scientific Data Repositories’) (213037).

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