Question: Number Of Synonymous Vs. Nonsynonymous Mutations Between Species (Ensembl)
0
gravatar for Max
5.6 years ago by
Max130
Max130 wrote:

I've seen several papers citing a database/tool in Ensembl that allows one to select to species and compute the number of synonymous vs. non-synonymous substitutions over the entire genome (insofar as alignment is possible) and gene by gene. I'm unable to find this option when searching Ensembl, so if somebody could provide the link I would greatly appreciate it.

I would assume that it's somewhere in this section, but can't find the specific application: http://useast.ensembl.org/info/website/tutorials/compara.html

Thank you in advance.

ensembl • 2.0k views
ADD COMMENTlink modified 5.6 years ago by Biojl1.7k • written 5.6 years ago by Max130

Are you looking after dN/dS ratio and comaprison between sps. ?

ADD REPLYlink written 5.6 years ago by aravind ramesh510

Yes, basically.

ADD REPLYlink written 5.6 years ago by Max130
1
gravatar for Biojl
5.6 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

Hi,

Gene by gene is rather easy. Just go to one gene of your interest and in the left menu select comparative genomics, then orthologs. The dN/dS column will give you the information for that gene. For IR1: http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000169047;r=2:227596033-227664475

If you are analyzing lots of gene I would advice you to do your own alignments and calculate that measure (and check them manually or automatically for strange values), since the alignments between orthologous genes in Ensembl are not very good sometimes.

ADD COMMENTlink written 5.6 years ago by Biojl1.7k

Thanks. To get a rough estimate, is there some way that I can just feed in a list of genes by hgnc id etc. and obtain the #synonymous/#non-synonymous between the two species?

ADD REPLYlink written 5.6 years ago by Max130
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