Question: Matching genomic positions to protein funtional/sctructural domains
0
gravatar for luisantome
4.2 years ago by
luisantome50
Spain
luisantome50 wrote:

Hi there,

I wish to annotate genomic variants with some kind of information related to protein conserved domains and (specially) functional domais to predict their potential role in human disease.

I was googling on the USCS genome browser and I found some tables that I could use with ANNOVAR or VEP (CCDS, Conserved,etc.). Do you know out there any other resource?

Thanks a lot!

ADD COMMENTlink modified 6 months ago by Biostar ♦♦ 20 • written 4.2 years ago by luisantome50
4
gravatar for rbagnall
4.2 years ago by
rbagnall1.4k
Australia
rbagnall1.4k wrote:

dbNSFP_variant database (https://sites.google.com/site/jpopgen/dbNSFP) contains a lot of annotations for all possible non-synonymous SNPs. The annotations include annotated protein structural/functional domains  "Interpro_domain"

dbNSFP can be downloaded here (~7.5GB):

ftp://ftp.scripps.edu/incoming/asu/dbNSFPv2.9.zip

But perhaps have a look at the README first to see what is included:

https://drive.google.com/file/d/0B60wROKy6OqcLXhCMEFaWE52X0U/view

 

 

ADD COMMENTlink written 4.2 years ago by rbagnall1.4k

thank you so much rbagnall for your comment. that's exactly what I was looking for

ADD REPLYlink written 4.2 years ago by luisantome50
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