Biostar Beta. Not for public use.
Synonymous And Non-Synonymous Snps
5
Entering edit mode
5.9 years ago
Elena • 240
@Elena1112

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

snp non • 54k views
ADD COMMENTlink
15
Entering edit mode
10.0 years ago
@Lars Juhl Jensen504

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
1
Entering edit mode

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
0
Entering edit mode

Thanku i think i can make something out of it

ADD REPLYlink
0
Entering edit mode

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

ADD REPLYlink
0
Entering edit mode

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
8
Entering edit mode
10.0 years ago
@Giulietta - Ensembl Helpdesk966

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
0
Entering edit mode

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
6
Entering edit mode
10.0 years ago
@Larry_Parnell559

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
5
Entering edit mode
10.0 years ago
Pablo ♦ 1.9k
@Pablo1002

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

ADD COMMENTlink
0
Entering edit mode

I am unable to download it

ADD REPLYlink
0
Entering edit mode

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
0
Entering edit mode
5.9 years ago
@mandecent.gupta16297

Can snpeff be used for predicing sysnonymous non synonymous?

ADD COMMENTlink
0
Entering edit mode

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
0
Entering edit mode
5.9 years ago
HG ♦ 1.1k
@HG7748

Yes it can be.

ADD COMMENTlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.3