Hi all,
I'm trying to calculate synonymous substitution rates to date whole-genome duplications. I understand how to calculate synonymous substitution rates, but where I am struggling is how to know which genes I should be comparing.
I identified genes in my species that I believe are duplicated and found orthologs of these genes in output from OrthoFinder. The problem is, the WGD event should have occurred after the species split from its closest relative (rice), yet I find evidence of this duplication in more distantly related species.. I can filter those out relatively easily, but I am still left with genes that I am unsure of how to decide which is ancestral and which is derived.
I'm trying to do this as autonomously as possible.. Of course, I could do this manually for a few genes, but I don't want to do it manually for 1000+ genes. Naturally, that wouldn't pass peer-review either...
It's super simple to filter gene names using regular expressions in Python, but being precise is a much more difficult task. I could collect all of the genes I am interested in in a dictionary, but the matter of figuring out which genes to include is maddening. Has anyone achieved this before? Maybe using BLAST?
Alignments are being done with Clustal Omega, backtranslation with a custom script, and calculation of synonymous substitution values with PAML.
Thanks in advance.
Matthew
I'm trying to calculate synonymous substitution rates to date whole-genome duplications. I understand how to calculate synonymous substitution rates, but where I am struggling is how to know which genes I should be comparing.
I identified genes in my species that I believe are duplicated and found orthologs of these genes in output from OrthoFinder. The problem is, the WGD event should have occurred after the species split from its closest relative (rice), yet I find evidence of this duplication in more distantly related species.. I can filter those out relatively easily, but I am still left with genes that I am unsure of how to decide which is ancestral and which is derived.
I'm trying to do this as autonomously as possible.. Of course, I could do this manually for a few genes, but I don't want to do it manually for 1000+ genes. Naturally, that wouldn't pass peer-review either...
It's super simple to filter gene names using regular expressions in Python, but being precise is a much more difficult task. I could collect all of the genes I am interested in in a dictionary, but the matter of figuring out which genes to include is maddening. Has anyone achieved this before? Maybe using BLAST?
Alignments are being done with Clustal Omega, backtranslation with a custom script, and calculation of synonymous substitution values with PAML.
Thanks in advance.
Matthew