Question: Obtaining Non Horse Ref Seq Genes
gravatar for modi2020
7.2 years ago by
United States
modi202040 wrote:

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

ucsc • 1.4k views
ADD COMMENTlink modified 7.2 years ago by Devon Ryan97k • written 7.2 years ago by modi202040
gravatar for Devon Ryan
7.2 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

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.

ADD COMMENTlink written 7.2 years ago by Devon Ryan97k

Thank you so much.

I will give that a try!

Best wishes

ADD REPLYlink written 7.2 years ago by modi202040
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