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Interpro2GO specifications

Information


Unique identifier OMICS_14665
Name Interpro2GO
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Maintainer


  • person_outline Robert Finn

Publication for Interpro2GO

Interpro2GO citations

 (50)
library_books

An Updated Functional Annotation of Protein Coding Genes in the Cucumber Genome

2018
Front Plant Sci
PMCID: 5863696
PMID: 29599790
DOI: 10.3389/fpls.2018.00325

[…] species or in newly sequenced genomes rely on homology transfer based on sequence similarity, including blast2go (conesa et al., ), identification of conserved domains (rentzsch and orengo, ) and interpro2go (burge et al., ). in addition, orthomcl (li et al., ) has been used to identify orthologous relationships between several related genomes using the bidirectional best hits (bbh) strategy […]

library_books

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy P Framework

2018
Proteomes
PMCID: 5874766
PMID: 29385081
DOI: 10.3390/proteomes6010007

[…] annotations from these databases to experimentally identified proteins are often database-specific, such as the eggnog-mapper [] and interproscan []. in addition, megan6 can be used to carry out interpro2go, kegg, seed and eggnog analysis to determine the distribution of functions amongst expressed proteins in the microbiome []. , beyond mapping functional annotations to identified proteins, […]

library_books

Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree

2017
GigaScience
PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] using interproscan 5 (interproscan, rrid:scr_005829) [] for pfam domains, panther, enzyme comissioned number (ec), and kegg categories. gene ontology annotation was obtained, where possible, from interpro2go and ec2go mappings., sequencing of the h. impetiginosus tree genome generated c. 599 million reads, comprising 73 gbp of sequence data. this represents nearly ×132 the expected sequence […]

library_books

Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

2017
Genome Biol Evol
PMCID: 5739047
PMID: 29220487
DOI: 10.1093/gbe/evx255

[…] between those method results and go terms as provided by uniprot-goa for electronic annotation methods (http://www.ebi.ac.uk/goa/electronicannotationmethods, last accessed december 7, 2017): interpro2go, hamap2go, ec2go, uniprotkeyword2go, uniprotsubcellular_location2go. the annotation data set was limited to the electronically inferred data to avoid biases in the annotation of certain […]

library_books

Development of an Efficient Protein Extraction Method Compatible with LC MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis

2017
Front Plant Sci
PMCID: 5559503
PMID: 28861098
DOI: 10.3389/fpls.2017.01416

[…] calculated using the expasy tool (http://web.expasy.org/compute_pi/). the identified proteins were further annotated using interproscan (finn et al., ). the gene ontology terms were inferred using interpro2go (gene ontology consortium, ). subcellular localization of the proteins was assigned using plant-mloc (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/) and manually translated to gene […]

library_books

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant parasitic nematodes

2017
PLoS Genet
PMCID: 5465968
PMID: 28594822
DOI: 10.1371/journal.pgen.1006777

[…] and parameters. a gene ontology annotation was inferred from the pfam protein domain annotation using the pfam2go mapping file maintained at the gene ontology portal and generated from the interpro2go mapping []. gene ontology terms were also mapped on the generic go-slim ontology using the goslimviewer utility developed as part of agbase []., the duplicated structures of meloidogyne […]


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Interpro2GO institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Faculty of Life Science and School of Computer Science, The University of Manchester, Manchester, UK; Swiss Institute of Bioinformatics (SIB), CMU, Geneva, Switzerland; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Department of Biochemistry, University of Geneva, Geneva, Switzerland; Pôle Rhone-Alpin de Bio-Informatique (PRABI), Universite Claude Bernard, Villeurbanne, France; European Molecular Laboratory (EMBL), Heidelberg, Germany; Department of Computer Science, University of Bristol, Bristol, UK; J. Craig Venter Institute (JCVI), Chinakville, MD, USA; Protein Information Resource (PIR), Georgetown University Medical Center, WA, DC, USA; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA; Structural and Molecular Biology Department, University College London, University of London, London, UK; Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
Interpro2GO funding source(s)
Supported by Biotechnology and Biological Sciences Research Council (BBSRC) [BB/L024136/1]; European Molecular Biology Laboratory (EMBL) core funds.

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