Question: How to calculate the conservation score of a gene
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gravatar for yunzhe.jiang97
13 days ago by
yunzhe.jiang970 wrote:

Hi!

I am a freshman at comparative genomics. Now, I've got several sequences of genes, and I want to calculate the conservation scores of these genes. Is anyone familiar with the calculation of conservation scores? It would be nice if someone can provide a pipeline. Thanks very much.

comparative geneomics • 100 views
ADD COMMENTlink modified 8 days ago by reza.jabal420 • written 13 days ago by yunzhe.jiang970

A must read: https://www.jstor.org/stable/2461605?seq=1 (A epic Acknowledgments section). tl;dr: You have to have a phylogenetic tree. In addition, conservation of what? Of each position? of the entire gene?

ADD REPLYlink written 12 days ago by Asaf8.3k

Thanks for your reply. I want to calculate the conservation score of a gene.

ADD REPLYlink written 12 days ago by yunzhe.jiang970

What do you mean by calculation? Do you want to calculate conservation scores from scratch or you just want to annotate your gene list with pre-calculated conservation scores? There are multiple resources for pre-calculated conservation scores. Such as GERP and Phylop to name a few!

ADD REPLYlink written 12 days ago by reza.jabal420

Yeah. I do need to annotate my gene list with a pre-calculated conservation score.

ADD REPLYlink written 12 days ago by yunzhe.jiang970
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gravatar for reza.jabal
8 days ago by
reza.jabal420
New York, USA
reza.jabal420 wrote:

There are a few well-established annotation software that accepts multiple input format and annotates your genes/variants with pathogenicity and conservation metrics from different methods/databases.

If you're not familiar with command-line scripting, I recommend taking a look at VEP and wANNOVAR.

ADD COMMENTlink written 8 days ago by reza.jabal420
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