InterProScan: protein domains identifier

By Emmanuel Quevillon, Ville Silventoinen, Sharmila Pillai, Nicola Harte, Nicola J. Mulder, Rolf Apweiler, Rodrigo Lopez. Nucleic Acids Res., 2005

2,907 citations recorded by the source corpus.

InterProScan [E. M. Zdobnov and R. Apweiler (2001) Bioinformatics, 17, 847–848] is a tool that combines different protein signature recognition methods from the InterPro [N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bradley, P. Bork, P. Bucher, L. Cerutti et al. (2005) Nucleic Acids Res., 33, D201–D205] consortium member databases into one resource. At the time of writing there are 10 distinct publicly available databases in the application. Protein as well as DNA sequences can be analysed. A web-based version is accessible for academic and commercial organizations from the EBI (). In addition, a standalone Perl version and a SOAP Web Service [J. Snell, D. Tidwell and P. Kulchenko (2001) Programming Web Services with SOAP, 1st edn. O'Reilly Publishers, Sebastopol, CA, ] are also available to the users. Various output formats are supported and include text tables, XML documents, as well as various graphs to help interpret the results.

Subfields: Molecular Biology

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Citations in the corpus

agriGO: a GO analysis toolkit for the agricultural community (2010, methodology): “We run BLAST (25), Pfam (26) or InterProScan (27) to generate GO annotation for those publicly unsupported identifiers with sequences.”
New developments in the InterPro database (2007, methodology): “All matches of the protein signatures contributed by member databases against the UniProt Knowledgbase (UniProtKB) (13) are calculated using the InterProScan software (14), which integrates the search algorithms from the member databases into a single package.”
The EMBL-EBI bioinformatics web and programmatic tools framework (2015, methodology): “Legacy applications SRS (23), InterProScan 4 (24) and NCBI BLAST (non-plus) have been retired.”
MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. (2019, methodology): “Merca-tor4 and InterProScan inferences were compared with the gold standard annotation, and resulted in a Matthews Correlation Coefﬁcient (MCC) of 0.16 for both Mercator4 and InterProScan (with Mercator4 yielding a slightly higher value), indicating that GO terms inferred are indeed meaningful and n”
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways (2006, methodology): “The InterProScan software (15,16), freely available at http://www.”
FungiDB: an integrated functional genomics database for fungi (2011, methodology): “Genomes and annotation in FungiDB are processed through the same analysis pipeline, which provides additional data, including InterPro domains (26), gene ontology term association (27), signal peptide predictions (28), transmembrane domain predictions, open reading frame predictions, BLAST against t”
Identification of protein secretion systems in bacterial genomes (2015, methodology): “The family of TssQ proteins matched no PFAM profile, but using InterProScan we could predict the presence of one secretion signal and its cellular localisation at the outer-membrane 91,92 .”
InterPro in 2011: new developments in the family and domain prediction database (2011, methodology): “InterPro signature matches to the UniProt Knowledgebase (UniProtKB) (17) and the UniParc protein sequence archive are calculated using the InterProScan software package (18).”
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea (2011, methodology): “The first criterium was based on identification of functional domains (e.g. InterProScan, CDD) or topology/targeting domains (e.g. Sig-nalP, TargetP, TMHMM) (see M7).”
InterPro: the integrative protein signature database (2008, methodology): “The coverage of various sequence databases by InterPro signatures is shown in Table 1. InterPro signature matches to the UniProt Knowledgebase [Uni-ProtKB; (12)] are regularly calculated using the Inter-ProScan software package ( 13 ) and this information is used to aid UniProtKB curators in their a”
A new bioinformatics analysis tools framework at EMBL–EBI (2010, methodology): “These include sequence similarity search services (http://www.ebi.ac .uk/Tools/similarity.html), such as FASTA (3), BLAST (4,5) and InterProScan (6) and multiple sequence alignment tools (http://www.ebi.ac.uk/Tools/sequence.html), such as ClustalW (7), T-Coffee (8), MUSCLE (9), Kalign (10) and MAFFT”
InterProScan 5: genome-scale protein function classification (2014, background): “In common with earlier versions, InterProScan 5 has been designed to allow the efficient characterization of relatively small numbers of sequences in a single analysis, including the ability to parallelize search jobs to minimize wall-clock time (as opposed to CPU time).”