Variant functional detection software tools | High-throughput sequencing data analysis
Modern sequencing technologies produce increasingly detailed data on genomic variation. However, conventional methods for relating either individual variants or mutated genes to phenotypes present known limitations given the complex, multigenic nature of many diseases or traits.
Predicts functional consequences of non-synonymous single nucleotide polymorphisms (nsSNP). FATHMM is built on a sequence-based method that associates evolutionary conservation in homologous sequences with disease-specific weights. This software can characterize mutations related to a specific disease, or a group of related diseases (disease-specific), and other putative disease-causing (non-specific) mutations.
Allows statistical phylogenetic modeling and functional element identification. PHAST is a collection of programs and supporting libraries for comparative genomics. The software also provides methods for detecting departures from neutrality in rates and patterns of molecular evolution. It is well-suited for analyzing patterns of conservation and acceleration in aligned sequences, and for extracting data from or exporting data to the UCSC Genome Browser and related resources, such as Galaxy.
Determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Simply input the coordinates of your variants and the nucleotide changes to find out the genes and transcripts affected by the variants, location of the variants (e.g. upstream of a transcript, in coding sequence, in non-coding RNA, in regulatory regions), consequence of your variants on the protein sequence (e.g. stop gained, missense, stop lost, frameshift); known variants that match yours, and associated minor allele frequencies from the 1000 Genomes Project, SIFT and PolyPhen scores for changes to protein sequence.
Performs identification of constrained elements in multiple alignments, by quantifying substitution deficits. GERP is a bottom-up method for constrained element detection that identifies sites under evolutionary constraint, i.e., sites that show fewer substitutions than would be expected to occur during neutral evolution. The software then aggregates these sites into longer, potentially functional sequences called constrained element. It is suitable for high-throughput analysis of genomic data.
Annotates and predicts the effects of single nucleotide polymorphisms (SNPs). SnpEff features include: (1) the ability to make thousands of predictions per second; (2) the ability to add custom genomes and annotations; (3) the ability to integrate with Galaxy (4) compatibility with multiple species and multiple codon usage tables, (5) integration with Broad's Genome Analysis Toolkit (GATK) and (6) the ability to perform non-coding annotations. It enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.
Assists researchers to perform evaluation of the pathogenic potential of DNA sequence alterations. MutationTaster is an online application that aims to determine the functional consequences of amino acid substitutions, short insertion and/or deletion (indel) mutations, variants spanning intron-exon borders, intronic and synonymous alterations. Moreover, this tool is able to categorize confirmed polymorphisms and known disease mutations.
Predicts the possible impact of an amino acid substitution on the structure and function of a human protein. PolyPhen predicts the functional significance of an allele replacement from its individual features by a Naïve Bayes classifier. The web application allows users to (i) predict the effect of a single-residue substitution or reference single nucleotide polymorphism SNP, (ii) analyze SNPs in a batch mode, and (iii) search in a database of precomputed predictions for the whole human exome sequence space.