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.
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.
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.
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.
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.
Provides a suite of methods important for the prediction of protein structural and functional features. predictProtein is a web server that incorporates over 30 tools. This software searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function. It can help when little is known about the protein in question. For medium-to-high throughput analyses, downloadable software packages and the PredictProtein Machine Image (PPMI) are available.
Calculates nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging. KaKs Calculator implements a set of candidate models in a maximum likelihood framework. It employs the Akaike information criterion to measure fitness between models and data. This tool aims to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences.
A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important. The performance of PROVEAN is comparable to popular tools such as SIFT or PolyPhen-2.