Question: splice site mutations
3
gravatar for bioguy24
6.1 years ago by
bioguy24190
Chicago
bioguy24190 wrote:

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.

forum next-gen database • 1.7k views
ADD COMMENTlink modified 6.1 years ago by Pierre Lindenbaum129k • written 6.1 years ago by bioguy24190
3
gravatar for Charles Warden
6.1 years ago by
Charles Warden7.8k
Duarte, CA
Charles Warden7.8k wrote:

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.

ADD COMMENTlink written 6.1 years ago by Charles Warden7.8k
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