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.

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.

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.

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

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.

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.

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

MutationTaster evaluates disease-causing potential of sequence alterations.

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.

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.