Article

Spliceman-a computational web server that predicts sequence variations in pre-mRNA splicing

Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02903, USA.
Bioinformatics (Impact Factor: 4.62). 02/2012; 28(7):1031-2. DOI: 10.1093/bioinformatics/bts074
Source: PubMed

ABSTRACT It was previously demonstrated that splicing elements are positional dependent. We exploited this relationship between location and function by comparing positional distributions between all possible 4096 hexamers around a database of human splice sites. The distance measure used in this study found point mutations that produced higher distances disrupted splicing, whereas point mutations with smaller distances generally had no effect on splicing. Reasoning the idea that functional splicing elements have signature positional distributions around constitutively spliced exons, we introduce Spliceman-an online tool that predicts how likely distant mutations around annotated splice sites were to disrupt splicing. Spliceman takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation included the analyses of 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish.
Freely available on the web at http://fairbrother.biomed.brown.edu/spliceman/
fairbrother@brown.edu.

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    • "Primer sequences and PCR conditions are available upon request. The Spliceman web server (Lim and Fairbrother, 2012) was used to estimate the pathogenicity of the splice-site mutation identified in patient 3. "
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