Our Other Tools
Univeral Mutation Databases
The UMD databases are hosted at INSERM UMR_S910. These tools are dedicated to the collection of mutations in human genes associated with genetic diseases. Most of these locus specific databases are freely accessible but some can only be accessed by a password.
UMD High Throughput Sequencing
We decided to create the UMD-HTS resource to allow the prediction of the best candidate pathogenic mutations from a list of any human SNP. The UMD-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). The user can use UMD-HTS either to analyze a list of SNPs or to directly access predictions for a given gene or a genomic region.
Next generation sequencing technologies generate a large amount of data. On average around 70,000 variations can be identified using Whole Exome sequencing technologies. Among these, one to two variations correspond to pathogenic mutations responsible for a human genetic disease. Therefore it is crucial to identify and limit downstream analysis to a handful amount of potential candiates. Consequently we habe developped a computational method based on a combinatorial approach which allows the scoring of exonic nucleotide substitutions throughout the human genome to identify potential causative mutations.
Human Splicing Finder
In order to better understand intronic and exonic mutations leading to splicing defects, we decided to create the Human Splicing Finder website. This tool is aimed to help studying the pre-mRNA splicing. To calculate the consensus values of potential splice sites and search for branch points, new algorithms were developed. Furthermore, we have integrated all available matrices to identify exonic and intronic motifs, as well as new matrices to identify hnRNP A1, Tra2-β and 9G8.