Question: Position of SNPs with respect to codon
0
gravatar for Chirag Nepal
3.3 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

Hi all,

I am trying to plot the position of SNP with respect to the codon position, to see, if there is an enrichment in 3rd position of the codon or 1st position. It is easy to do, but i did not find the genomic coordinates of codon (in 3 nt intervals). I only find the CDS coordinates from UCSC. Is there available information of codon coordinates that can be downloaded.

 

Thanks !!

 

trna snp codon • 1.1k views
ADD COMMENTlink modified 4 weeks ago by rtasakis0 • written 3.3 years ago by Chirag Nepal2.2k

I'm interested in the exact same thing. Do you guys know how could this be transferrable to R?

Thanks in advance, R

ADD REPLYlink written 4 weeks ago by rtasakis0

What have you tried?

ADD REPLYlink written 28 days ago by RamRS21k
0
gravatar for RamRS
3.3 years ago by
RamRS21k
Houston, TX
RamRS21k wrote:

Codon positions are usually easily derivable from CDS positions. Use the formula x mod 3. The result can be 1 (base #1), 2 (base #2) or 0(base #3) of a codon.

ADD COMMENTlink written 3.3 years ago by RamRS21k

Aware of any awk/perl scripts that does, first add codon number (codon1, codon2 and so on) from CDS sequence, and subsequently add base position (#1 or #2 or #3) within each codon. 
 

ADD REPLYlink written 3.3 years ago by Chirag Nepal2.2k

It's a mathematical formula. Codon number is ceiling(cds_coord/3) and base number is cds_coord mod 3 == 0 ? 3 : cds_coord mod 3

You can write a simple script that does this math. If you're new to scripting, this would be a good time to start.

ADD REPLYlink written 3.3 years ago by RamRS21k
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