Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor

By W. Mclaren, Bethan Pritchard, Danielle Rios, Yuan Chen, Paul Flicek, Fiona Cunningham, Alfonso Valencia

1,610 citations recorded by the source corpus.

Summary: A tool to predict the effect that newly discovered genomic variants have on known transcripts is indispensible in prioritizing and categorizing such variants. In Ensembl, a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all Ensembl and Ensembl Genomes supported species. Availability: The Ensembl SNP Effect Predictor can be accessed via the Ensembl website at http://www.ensembl.org/. The Ensembl API (http://www.ensembl.org/info/docs/api/api_installation.html for installation instructions) is open source software. Contact: wm2@ebi.ac.uk; fiona@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

Better prediction of functional effects for sequence variants (2015, neutral): “Some tools are focused on non-coding regions [2-4]; others focus on coding regions and predict the effects of single amino acid variants (non-synonymous single-nucleotide polymorphisms, nsSNPs, or single amino acid substitutions, SAAS) on aspects such as protein structure [5], stability [6-8], bindi”
A general framework for estimating the relative pathogenicity of human genetic variants (2014, methodology): “5; Supplementary Figure 16; Supplementary Note), likely due to the increased ability of larger studies and stronger association statistics to enrich for causal variants.”
Ensembl 2011 (2010, methodology): “…we encourage incorporation of our code base and data into third party resources as well as the programmatic use of our results in external analysis pipelines that interact with these results using the Ensembl API (8), Ensembl tools such as the SNP Effect Predictor (9) and the Ensembl BioMart (10).”
Ensembl 2015 (2014, methodology): “For example, for the VEP, users can submit up to 1000 variants in one request (i.e. 15 000 variants per second) a 5000-fold increase over the VEP annotation rate on the beta server.”
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR (2015, methodology): “In general, these tools can be accessed either through command line (for example, VEP 15 , VAAST 17 , pVAAST 37 , AnnTools 18 , SnpEff 38 and GEMINI 39 ) or on the web (for example, VAT 40 , SeattleSeq 41 , AVIA 42 and VARIANT 43 ).”
The UCSC Genome Browser database: 2015 update (2014, methodology): “Users can upload variants in a variety of formats: dbSNP rs identifiers, VCF and pgSNP format and obtain output as HTML views or tab-separated text in Ensembl Variant Effect Predictor format (22).”
WormBase 2016: expanding to enable helminth genomic research (2015, methodology): “This has allowed us to provide a number of tools developed for the Ensembl project with little or no modification, for example the Variant Effect Predictor (23), and REST application programming interface (24).”
Ensembl 2012 (2011, methodology): “The Variant Effect Predictor (42) has also been extended to include these features and as an option, to run as a stand-alone software program that does not require a network connection or Ensembl database.”
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer (2014, methodology): “A number of tools have been developed using these data to annotate potential regulatory variants or to suggest the most likely causal variants in linkage disequilibrium with GWAS SNPs, such as Haploreg [18], RegulomeDB [19], ANNOVAR [20], GEMINI [21], FunciSNP [22], and VEP [23].”
VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants (2014, methodology): “The ensemblVEP package is an interface to the VEP (McLaren et al ., 2010) tool, while functions in VariantAnnotation allow close integration with SNP analysis routines in packages such as snpStats .”