Question: How to retrieve splicing information for a Human gene?
0
gravatar for twinstar2
3.0 years ago by
twinstar20
twinstar20 wrote:

Hi,

I have mutations with an absolute Position, Chromosome and context e.g.:

Chr Pos Ref Alt Context
chr21 36252877 C T Coding,Intergenic

So i found out with my python script, that it's in this example the gene DOPEY2 and now I am searching for a way to get all possible protein sequences that are affected by this mutation.
Any help is appreciated.

PS: I downloaded the hg19 genome and gathered the DNA Sequences of the genes, but i need the splicing informations for further progress.

Update: I still don't know the exact solution, but for anyone with a similar problem, have a look at ANNOVAR Documentation,Coding_Change

ensembl • 759 views
ADD COMMENTlink modified 2.9 years ago • written 3.0 years ago by twinstar20
2
gravatar for WouterDeCoster
3.0 years ago by
Belgium
WouterDeCoster41k wrote:

You probably want to use a variant effect predictor like SnpEff, Annovar or VEP for this job.

ADD COMMENTlink written 3.0 years ago by WouterDeCoster41k
0
gravatar for twinstar2
2.9 years ago by
twinstar20
twinstar20 wrote:

VEP is not useful for my case, i already have nearly all the information VEP can provide.
But Annovar looks promising, this thing is HUGE.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by twinstar20

Please use ADD COMMENT to reply to earlier answers, as such this thread remains logically structured and easy to follow.

I wasn't aware that Annovar provided more information than VEP, but good that you found what you need.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by WouterDeCoster41k
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