How to calculate protein length according to SNP position

Question

[hntiger1688]

Hi,

I am doing a bioinformatics project. Now, I get the thousands of insertion deletion SNPs. All of the SNPs are in the coding region. I know the SNP position, gene name and gene location of SNPs. I want to get the percentage of protein length with and without the SNPs.

(For example, if the gene has the SNP, the length of protein is 100 amino acids. If the gene doesn't have the SNP, the length will be 1000 amino acids. So the percentage of length will be 100/1000= 10%.)

So how can I do that by R or is there any software can do it?

Ron

[Ashutosh Pandey]

SNPs won't produce change in protein lengths unless they are nonsense or disrupt the stop-codon. In other words, majority of SNP changes will only produce synonymous/nonsynonymous changes that won't affect amino acid lengths. Indels (Insertions or deletions) can cause frameshift mutations that can increase or decrease the length of the protein. Please go through some paper that describe different variant types and then modify your question to make it more clear.

Answer 1

[Ram]

Like Ashutosh said, you might wanna brush up on possible effects of coding variants on the amino acid sequence.

A few possible effects (off the top of my head) are synonymous and non-synonymous (mis-sense as well as non-sense), gain-of-stop and loss-of-stop, frameshift, splice site donor/acceptor mutations.

You might wanna use software such as snpEff to predict the effect of various variants and then use a simple awk to pick appropriate effects. For each type of mutation, you might then wish to calculate the new stop position or the frameshift - I'd suggest translating the mutant mRNA sequence to avoid manual work. And then, you'd calculate the length of this mutant protein and compare it to wild type.

So while you can look for a set of software to help you with each step of the analysis, IMHO there is no one-stop solution that will help you end to end with no customization.

[hntiger1688]

Thank you!