snv to codon change

Question

[2nelly]

Hi all,

Does anybody know a tool to display the codon changes caused by a specific list of snv's. I am not interesting for the amino acid changes.

I want something like that for instance: chr7 12771690 G A exonic Zscan18 ---------> TGC>TAC

Thanks in advance!

Answer 1

[Ibrahim Tanyalcin]

Dear,

I have published a tool for this, however it is gene centric, meaning that SNVs are displayed per gene. Here are some example outputs:

http://i-pv.org/EGFR.html

http://i-pv.org/JAK2.html

You can either click o the SNVs or use the lotus view tool. First turn on the amino acids you want to see and than click the icon that pops out. It is explained here:

http://i-pv.org/gifs/lotus.gif

[GenoMax]

Where can one find that tool? Or does one just replace gene names in the example links you have posted?
Looks like that is it. Use your gene name in http://i-pv.org/HGNC_NAME.html

[Ibrahim Tanyalcin]

Dear,

I did not create a database for all the genes. Some people want to use it for a specific set of variations, or some people use their VCF files. I used the Biomart variation database. So, eventually you will need to generate your own graph. I posted the tutorials on the webpage. You will need your mRNA, protein sequence in fasta format and your variation file. If you are interested in a certain gene, let me know. I'll generate it and put it online.