Computational protocol: A Splice Mutation and mRNA Decay of EXT2 Provoke Hereditary Multiple Exostoses

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Protocol publication

[…] The EXT2 gene sequences from 43 different species were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/). Multiple sequence alignments were performed using ClustalX with standard settings .Bioinformatics analysis of potential splicing aberrations was done using two different web-based programs designed to detect putative splice sites, taking into account branch points, exonic and intronic motifs, and several regulatory proteins. CRYP-SKIP (http://cryp-skip.img.cas.cz/) was used to estimate the probability of cryptic splice-site activation (PCR-E) and exon skipping (1-PCR-E) as a result of splicing mutations . The CRYP-SKIP algorithm uses a multiple logistic regressions to perform splice site prediction from a mutated sequence. The splice site prediction program at BDGP (http://www.fruitfly.org/about/index.html) was used to predict cryptic splice sites and the influence on splice sites in the mutant sequence . The BDGP algorithm uses a generalized hidden Markov model to recognize donor and acceptor sites. […]

Pipeline specifications

Software tools Clustal W, CRYP-SKIP
Databases BDGP
Application WGS analysis
Organisms Homo sapiens
Diseases Exostoses, Multiple Hereditary, Genetic Diseases, Inborn