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Ensemble Variant Effect Predictor
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Ensemble Variant Effect Predictor

Ensembl Variant Effect Predictor predicts the effects of single nucleotide polymorphism (SNPs), copy number variation (CNV), and indels on genes, transcripts, protein, and regulatory sequences.



Ensemble Variant Effect Predictor

Ensembl Variant Effect Predictor predicts the effects of single nucleotide polymorphism (SNPs), copy number variation (CNV), and indels on genes, transcripts, protein, and regulatory sequences.

Topic

Genetics; Genetic variation; Function analysis; Genomics

Details

  • Operation: Protein modelling (mutation)
  • Input: A:
    1. chromosome - just the name or number, with no 'chr' prefix
    2. start
    3. end
    4. allele - pair of alleles separated by a '/', with the reference allele first
    5. strand - defined as + (forward) or - (reverse).
    6. identifier - this identifier will be used in VEP's output. If not provided, VEP will construct an identifier from the given coordinates and alleles.
    B:VCF; VCF - Structural variants; HGVS identifiers; Variant identifiers; Genomic SPDI notation; REST-style regions
  • Output: Uploaded variation; Location; Allele; Gene; Feature; Feature type; Consequence; Position in cDNA; Position in CDS; Position in protein; Amino acid change; Codon change; Co-located variation; Extra
  • Software interface: Command-line user interface; web user interface; Rest API
  • Language: Perl
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Apache License Version 2.0
    • Cost: Free
  • Version name: 97
    • Maturity: Mature
  • Credit: Wellcome Trust (grant numbers WT095908 and WT098051) and the European Molecular Biology Laboratory. This work has also received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement number 200754 (GEN2PHEN) and under grant agreement number 222664 (Quantomics), and from the European Union’s Horizon 2020 research and innovation programme under grant agreement number 634143 (MedBioinformatics).
  • Contact: wm2 _at_ ebi.ac.uk
  • Collection: EBI Tools

Publications

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. "The Ensembl Variant Effect Predictor." Genome Biology Jun 6;17(1):122. (2016). https://doi.org/10.1186/s13059-016-0974-4
PMID: 27268795
PMCID: PMC4893825


Madeira F, Madhusoodanan N, Lee J, Tivey ARN, Lopez R "Using EMBL-EBI Services via Web Interface and Programmatically via Web Services." Curr Protoc Bioinformatics. 2019 Apr 30:e74. https://doi.org/10.1002/cpbi.74
PMID: 31039604


Harte N, Silventoinen V, Quevillon E, Robinson S, Kallio K, Fustero X, Patel P, Jokinen P, Lopez R "Public web-based services from the European Bioinformatics Institute." Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W3-9. https://doi.org/10.1093/nar/gkh405
PMID: 15215339
PMCID: PMC441543


Pillai S, Silventoinen V, Kallio K, Senger M, Sobhany S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R. "SOAP-based services provided by the European Bioinformatics Institute." Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W25-8. https://doi.org/10.1093/nar/gki491
PMID: 15980463
PMCID: PMC1160251


Labarga A, Valentin F, Anderson M, Lopez R. "Web services at the European bioinformatics institute." Nucleic Acids Res. 2007 Jul;35(Web Server issue):W6-11. Epub 2007 Jun 18. https://doi.org/10.1093/nar/gkm291
PMID: 17576686
PMCID: PMC1933145


McWilliam H, Valentin F, Goujon M, Li W, Narayanasamy M, Martin J, Miyar T, Lopez R. "Web services at the European Bioinformatics Institute-2009." Nucleic Acids Res. 2009 Jul;37(Web Server issue):W6-10. https://doi.org/10.1093/nar/gkp302
PMID: 19435877
PMCID: PMC2703973


Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R. "A new bioinformatics analysis tools framework at EMBL-EBI." Nucleic Acids Res. 2010 Jul;38(Web Server issue):W695-9. https://doi.org/10.1093/nar/gkq313
PMID: 20439314
PMCID: PMC2896090


McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R "Analysis Tool Web Services from the EMBL-EBI." Nucleic Acids Res. 2013 Jul;41(Web Server issue):W597-600. https://doi.org/10.1093/nar/gkt376
PMID: 23671338
PMCID: PMC3692137


Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R "The EMBL-EBI bioinformatics web and programmatic tools framework." Nucleic Acids Res. 2015 Jul 1;43(W1):W580-4. https://doi.org/10.1093/nar/gkv279
PMID: 25845596
PMCID: PMC4489272


Chojnacki S, Cowley A, Lee J, Foix A, Lopez R "Programmatic access to bioinformatics tools from EMBL-EBI update: 2017." Nucleic Acids Res. 2017 Jul 3;45(W1):W550-W553. https://doi.org/10.1093/nar/gkx273
PMID: 28431173
PMCID: PMC5570243


Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, Basutkar P, Tivey ARN, Potter SC, Finn RD, Lopez R "The EMBL-EBI search and sequence analysis tools APIs in 2019." Nucleic Acids Res. 2019 Apr 12. pii: gkz268. https://doi.org/10.1093/nar/gkz268
PMID: 30976793


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