InterProScan pipeline

InterProScan specifications

Information


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.
Output format TSV,XML,JSON,GFF,HTML,SVG
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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Documentation


Maintainers


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

Additional information


http://www.ebi.ac.uk/interpro/training.html http://www.ebi.ac.uk/interpro/search/sequence-search

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

Documentation


Maintainers


This tool is not maintained anymore.

Additional information


http://www.ebi.ac.uk/interpro/training.html http://www.ebi.ac.uk/interpro/search/sequence-search

Publications for InterProScan

InterProScan IN pipelines

 (82)
2018
PMCID: 5804319
PMID: 29423345
DOI: 10.7717/peerj.4320

[…] first used the program ‘anvi-gen-contigs-database’ to profile prochlorococcus genomes, during which prodigal v2.6.3 (hyatt et al., 2010) with default settings identified open reading frames. we used interproscan v5.17-56 (zdobnov & apweiler, 2001) and eggnog-mapper v0.12.6 (huerta-cepas et al., 2016) outputs for our genes with the program ‘anvi-import-functions’ to import annotations […]

2018
PMCID: 5808209
PMID: 29467784
DOI: 10.3389/fpls.2018.00119

[…] same method., the orfs of gbana1 were determined using orf finder1, and the protein sequences were deduced on the basis of codon sequences. the conserved domains of gbana1 were predicted using the interproscan database (version 5.21) as described (li n.y. et al., 2017). the protein coding region of the nbs-lrr gene (at4g27220.1), orthologous to gbana1 in g. barbadense, was acquired by blastp […]

2017
PMCID: 5302831
PMID: 28187150
DOI: 10.1371/journal.pone.0171291

[…] (table 2)., the pipeline for identification of genes belonging to the mco family and annotation of laccases consisted of three steps: 1) proteomes of 26 black yeast-like isolates were searched using interproscan [19] (last accessed december, 2015) for proteins carrying the prosite multicopper oxidase signatures ps00079 and ps00080 as well as the cu-oxidase pfam domains pf00394, pf07731, […]

2017
PMCID: 5374754
PMID: 28386531
DOI: 10.1016/j.gdata.2017.02.014

[…] all predicted genes are annotated for gene ontology (go) using blast2go function annotation system [7], [8], according to sequence comparison with blastp and domains/motif identification with interproscan [7] and pfam [9]. the c. sojina genome encoded predominant potential genomic elements involved in mycelium related development. it is through the mycelium that a fungus absorbs nutrients […]

2017
PMCID: 5471245
PMID: 28615669
DOI: 10.1038/s41598-017-03860-0

[…] query sequence were retrieved and loaded into blast2go42 (version 2.8.0) for go43 mapping and annotation. the sequences without blast hits and un-annotated sequences were then selected to undergo an interproscan44 against ebi databases to retrieve functional annotations of protein motifs and merge the interproscan go terms to the annotation set. following annotation and annotation augmentation […]

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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