splice site mutations

Question

[bioguy24]

Hello,

Can someone recommend a hg19 splice site database in which the data can be parsed and then queried against by annovar. Does a site exist? Thanks.

Answer 1

[Charles Warden]

Actually, ANNOVAR provides some splice site information in the "Func" column of the exome/genome reports. If I recall, I believe MutationTaster also takes splice site predictions into account (and MutationTaster damaging predictions are included in the main ANNOVAR report).

Additionally, these are two programs that I am currently testing for this purpose:

MutPred-Splice:

http://mutdb.org/mutpredsplice/download.htm

http://genomebiology.com/2014/15/1/R19

Skippy:

http://research.nhgri.nih.gov/skippy/input.shtml

http://genomebiology.com/content/11/2/R20

I haven't had a chance to complete my testing, so I don't yet have an opinion about those programs. However, they looked like they could be potentially useful.