Various prediction tools

WebPCR version 0.50
This service simulate PCR given a list of sequences in FASTA or Genbank format.
The last sequence in the list is interpreted as template and the preceding ones as primers.

Online tool developped by Charles University, Prague, to analyse MLPA data. Please ignore the certificate error message.

The eMLPA web system performs processing and computational analysis of MLPA data from genetic analyzers (raw data).

eMLPA is a universal user interface for various types of MLPA kits. It offers variant methods of eMLPA data normalization and analysis. No local program installation is needed for analyses – the only pre-requisite is access to the Internet.

Align-GVGD is a freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. Align-GVGD is an extension of the original Grantham difference to multiple sequence alignments and true simultaneous multiple comparisons. Users can either supply their own protein multiple sequence alignments (in FASTA format) or else select from our small but growing library of alignments. We currently have alignments for ATM, BRCA1, BRCA2, CHEK2, and TP53. We also provide a link to the TCoffee web site, which gives an excellent set of tools for making protein multiple sequence alignments.

The aim of this program suite is to support checks of sequence variant nomenclature according to the guidelines of the Human Genome Variation Society.

PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein and protein-DNA binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges.

TraceHaplotyper
This program genotypes a tracefile that results from sequencing of two chromosomes, which one of them having a deletion preceding a SNP. In such case the phase of these markers can be determined.

BLAT quickly maps your sequence to the genome.
Directly callable from our sequencing software Gensearch.

This site produces an interactive visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and displays geometric and relative entropy calculations.

Pmut is a software aimed at the annotation and prediction of pathological mutations, and in particular at answering the following question: given a mutation happening at a specific location in a protein sequence, can we say whether it will be pathological (that is, a mutation that can lead to disease for the carrier) or non-pathological/neutral (no effect on the carrier's health)? Pmut is based on the use of different kinds of sequence information to label mutations, and neural networks to process this information (Ferrer-Costa et al., 2004). It provides a very simple output: a yes/no answer and a reliability index.

Evolutionary analysis of coding SNPs
Estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. It calculates the subPSEC (substitution position-specific evolutionary conservation) score based on an alignment of evolutionarily related proteins, as described in Thomas et al., 2003 and Thomas & Kejariwal, 2004.

SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations.

PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. Please, use the form below to submit your query.

SNPs3D is a website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis.

The UMD-Predictor algorithm aims to predict the pathogenicity of any cDNA variation. This algorithm was included in the UMD software. Previous analysis on about 1,000 different substitutions has revealed that this algorithm was the most efficient. 
The UMH-HTS resource contains data for all transcripts extracted from Ensembl (HG18-ensembl 54 release).

The predictions are based on a combinatorial approach that takes into account the location of the variation at the protein level, that is, in which domain and whether the amino acid is involved in a structural or biological function; it checks for the degree of conservation (data from SIFT); estimates the differences in biochemical properties between the WT and the substituted amino acid (data from BLOSUM62 and Yu’s Biochemical matrix) and finally,as it is well known that missense mutations can have an effect on mRNA splicing, it checks for a potential impact of the substitutions on splicing signals (donor and acceptor splice sites as well as ESE and ESS).

MutationTaster evaluates disease-causing potential of sequence alterations.

Hansa is a tool to predict the deleterious effects of a mutation by using 10 Neutral- Disease Mis-Sense Mutation Discriminatory (NDMSMD) features. This tool will classify the mutation either as “DISEASE” or “NEUTRAL”

SpliceCenter is a suite of user-friendly tools that evaluate the impact of gene splicing variation on specific molecular biology techniques. Each of the utilities has a Help panel and a link to populate a sample query.

Accurate validation, mapping and formatting of sequence variants using HGVS nomenclature 

To aid our variant interpretation process, we created an openly-available online tool to efficiently classify variants based on the evidence categories outlined in the article: Richards, et al. Standards and guidelines for the interpretation of sequence variants. 2015. This site displays the evidence categories and descriptions from Table 3 and Table 4 with simple checkboxes for selecting appropriate criteria. The site then incorporates the algorithm in Table 5 to automatically assign the pathogenicity or benign impact based on the selected evidence categories.