Synonymous And Non-Synonymous Snps

Question

[Elena]

How can one distinguish synonymous and non-synonymous SNPs from the observed location of the SNPs?

Answer 1

[Lars Juhl Jensen]

The answer to this follows directly from the definitions of synonymous and non-synonymous SNPs. To be a synonymous or a non-synonymous SNP, the SNP must fall inside a protein-coding region of the DNA (otherwise it is a noncoding SNP). A synonymous SNP is a coding SNP that does not change the protein sequence. A non-synonymous SNPT is one that changes the protein sequence. So what you have to check is if the SNP changes a codon to a different codon for the same amino acid, in which case it is a synonymous SNP, or if it changes the codon to one that codes for a different amino acid, in which case it is a non-synonymous SNP.

[Elena]

the definition which u've given is exactly correct but i m trying to implement it using perl programming and since there are large no. of sequences with thousands of nucleotides,i am unable to implement it.

[Elena]

Thanku i think i can make something out of it

[Payal]

ya... but there are large number of nucleotide sequences..

[Lars Juhl Jensen]

Payal, I fail to get your point ... how does there being many different nucleotide sequences affect the definition of what a synonymous/non-synonymous SNP is?

Answer 2

[Giulietta - Ensembl Helpdesk]

The variant effect predictor calculates whether or not a variation is synonymous, non-synonymous, or non-coding in different splice variants (transcripts) based on genomic location:

http://www.ensembl.org/tools.html

Hope that helps.

[Larry_Parnell]

Giulietta, thanks for adding the Ensembl perspective to some of the (many) BioStar questions. Good to have you as part of the conversation.

Answer 3

[Larry_Parnell]

A bit of a side topic here -

A SNP can change a splice site and that would change the resulting protein translation.

There can also be a situation where a SNP will be synonymous for one transcript isoform and nonsysnonymous for a different mRNA isoform. This could easily be true for genes transcribed from opposing strands.

Answer 4

[Pablo]

I've created snpEff to answer that kind of questions http://snpeff.sourceforge.net/ Let me know if that fits your needs.

[Payal]

I am unable to download it

[Pablo]

YOu have to click on the "Download" link

Here is the link for your convenience http://sourceforge.net/projects/snpeff/files/snpEff_v1_8.zip/download

[mandecent.gupta]

Can snpeff be used for predicting synonymous non synonymous?

[HG]

Yes it can be.

[Ashutosh Pandey]

Please use a new post to ask a new question. If you have a trivial "Yes" or "No" question you can use comments.