Question: Synonymous And Non-Synonymous Snps
5
gravatar for Elena
8.2 years ago by
Elena240
Elena240 wrote:

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

non snp • 53k views
ADD COMMENTlink modified 4.1 years ago by HG1.1k • written 8.2 years ago by Elena240
14
gravatar for Lars Juhl Jensen
8.2 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

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.

ADD COMMENTlink written 8.2 years ago by Lars Juhl Jensen11k
1

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.

ADD REPLYlink written 8.2 years ago by Elena240

Thanku i think i can make something out of it

ADD REPLYlink written 8.2 years ago by Elena240

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

ADD REPLYlink written 8.2 years ago by Payal150

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?

ADD REPLYlink written 8.2 years ago by Lars Juhl Jensen11k
8
gravatar for Giulietta - Ensembl Helpdesk
8.2 years ago by
Cambridge, UK

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.

ADD COMMENTlink written 8.2 years ago by Giulietta - Ensembl Helpdesk1.2k

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

ADD REPLYlink written 8.2 years ago by Larry_Parnell16k
6
gravatar for Larry_Parnell
8.2 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 8.2 years ago by Larry_Parnell16k
5
gravatar for Pablo
8.2 years ago by
Pablo1.9k
Canada
Pablo1.9k wrote:

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

ADD COMMENTlink written 8.2 years ago by Pablo1.9k

I am unable to download it

ADD REPLYlink written 8.2 years ago by Payal10

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

ADD REPLYlink written 8.2 years ago by Pablo1.9k
0
gravatar for mandecent.gupta
4.1 years ago by
United States
mandecent.gupta0 wrote:

Can snpeff be used for predicing sysnonymous non synonymous?

ADD COMMENTlink written 4.1 years ago by mandecent.gupta0

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

ADD REPLYlink written 4.1 years ago by Ashutosh Pandey11k
0
gravatar for HG
4.1 years ago by
HG1.1k
Germany
HG1.1k wrote:

Yes it can be.

ADD COMMENTlink written 4.1 years ago by HG1.1k
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