SilVA (Latin for “forest”) is a tool for the automated harmfulness prediction of synonymous (silent) mutations within the human genome. SilVA bases its predictions on a number of features, including conservation, codon usage, splice sites, splicing enhancers and suppressors, and mRNA folding free energy. Given variants in a VCF file, SilVA will rank the rare synonymous variants according to their predicted harmfulness.
- R package
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Bioinformatics. 2013 Aug 1;29(15):1843-50. doi: 10.1093/bioinformatics/btt308.
Identification of deleterious synonymous variants in human genomes.
Buske OJ, Manickaraj A, Mital S, Ray PN, Brudno M.