Obtaining Non Horse Ref Seq Genes

Question

[modi2020]

Hi guys,

I plan to conduct genome wide dN dS between human and hose genes based on the exons. I would like to use the human genes as a guide for this since the horse genome is really not well annotated. I would like to get the exon sequence of the human genes and the corresponding horse sequence. I have been trying to do that with the table browser but in vain. Can anyone please help guide me on how to go about this task?

I will be so grateful!

Thank you

Answer 1

[Devon Ryan]

You can obtain the human exon sequences (from the ensembl annotation, at least), quite easily with Biomart. Just click on "Sequence retrieval"->"Ensembl" and select the "Exon Sequences" radio button. You can then align the results against the horse genome. From the alignments, you could calculate dN/dS. There are probably other ways, but that would seem relatively straight forward.

[modi2020]

Thank you so much.

I will give that a try!

Best wishes