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Will a genetic mutation cause trouble? Ask Spliceman
Date:3/5/2012

PROVIDENCE, R.I. [Brown University] In a brief paper in the journal Bioinformatics, Brown University researchers describe a new, freely available Web-based program called Spliceman for predicting whether genetic mutations are likely to disrupt the splicing of messenger RNA, potentially leading to disease.

"Spliceman takes a set of DNA sequences with point mutations and computes how likely these single nucleotide variants alter splicing phenotypes," write co-authors Kian Huat Lim, a graduate student, and William Fairbrother, assistant professor of biology, in an "application note" published in advance online Feb. 10. It will appear in print in April.

Spliceman can be found at http://fairbrother.biomed.brown.edu/spliceman.

The software is based on research published last year in the Proceedings of the National Academy of Sciences, in which Fairbrother's group used Spliceman to show that perhaps as many as a third of the disease-causing mutations in the Human Genome Mutation Database do so by causing errant gene splicing.

Splicing of RNA, based on instructions in DNA, is like a film editing process. A gene includes raw footage and instructions on how it should be edited to produce a protein. If the editing instructions are faulty, the scenes extracted from the raw footage may be spliced together in the wrong order or the wrong scenes might be used.

Each of a person's 20,000 genes has about 20 splice sites. Sequences that regulate splicing often occur close to splice sites, and every possible "word" of DNA letters (e.g. AAA) has a signature distribution around the splice sites. But a mutation creates a new word. For example, an A-to-T mutation could change "AAA" to "ATA." In a normal genome, if AAA encodes proper splicing, its average distance to the nearest splice site will be short and if ATA doesn't encode proper splicing its distance would be longer.
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Contact: David Orenstein
david_orenstein@brown.edu
401-863-1862
Brown University
Source:Eurekalert

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