If a mutation is in the splice site (donor), how can we bioinformatically predict its function in silico? For example if the site is broken or not, is there any exon skipping, if no then how to find the next splice site?
it is impossible to predict function insilico, but expectation is very weak for the protein to maintain the proper function. ALl depends on the splice site.
you can try, or do a combination of complementary in silico tools to evaluate the mutations. just as Beston Nore said, it's difficult.
I having the same problem......
http://www.umd.be/HSF/#
but one can not defend this mutation without expression studies.
Hi, Amitabh,
several papers have adressed this issue and the reliability of predictions. My favourite is Houdayer et al., 2012. http://www.ncbi.nlm.nih.gov/pubmed/22505045 If you are interested, I can add some more interesting tips for papers.
Best regards, Lucie
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