URL: http://variant.bioinfo.cipf.es/
Proper Citation: VARIANT (RRID:SCR_005194)
Description: Analysis tool that can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. It not only reports the obvious functional effects in the coding regions but also analyzes noncoding SNVs situated both within the gene and in the neighborhood that could affect different regulatory motifs, splicing signals, and other structural elements. These include: Jaspar regulatory motifs, miRNA targets, splice sites, exonic splicing silencers, calculations of selective pressures on the particular polymorphic positions, etc. Software analysis pipelines used in the analysis of NGS data are highly modular, heterogeneous, and rapidly evolving. VARIANT can easily be incorporated into a NGS resequencing pipeline either as a CLI or invoked a webservice. It inputs data directly from the most widely used programs for SNV detection.
Abbreviations: VARIANT
Synonyms: Variant effect, VARIant ANalysis Tool
Resource Type: service resource, production service resource, data processing software, data analysis service, software application, analysis service resource, data analysis software, software resource
Defining Citation: PMID:22693211
Keywords: functional property, variant, gene, non-coding region, mirna, function, single nucleotide variant, next generation sequencing, command line
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