How to calculate the conservation score of a gene

Question

[yunzhe.jiang97]

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.

[Asaf]

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?

[yunzhe.jiang97]

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

[reza.jabal]

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!

[yunzhe.jiang97]

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

Answer 1

[reza.jabal]

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.