Hello everyone,
My research work on to find out the novel and polymorphisms in selected gene.. I found few novel and SNP'S..
Now I am going to write a review article on SNP'S and their effect (Genotype and Phenotype). I collected a data from previous literature. That data is on amino acid substitution (eg. p. D123R) what I have collected, but I would like to include nucleotide change (eg. c. 123A>G) and their rs no also for the easiest way to trace the data. I could request you to give a suggestion which tools are available to get the nucleotide change..
Thanks in advance
Hi Yedukondalu,
your question lacks some details as name of the gene and species you're working on but I'm sure that you'll find everything you're searching for at the UCSC database (http://genome.ucsc.edu). there are a lot of interesting tolls, but the table browser with selected filters will answer.
fred
If you have the amino acid changes as HGVS, you can put them in the Ensembl VEP:
http://www.ensembl.org/info/docs/tools/vep/index.html
This should get you the nucleotide change and the rsID, as well as the genomic location. Be aware, however, that amino acid changes can be ambiguous, and many different nucleotide changes can cause one amino acid change. There is more information about how the VEP can handle this in this blog post:
http://www.ensembl.info/2019/07/26/cool-stuff-the-ensembl-vep-can-do-parse-protein-hgvs/
Dear Frederic,
Thanks for your suggestion.
I am looking for human DUOX2 and NIS gene.
Best,
Yedukondalu K
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