Reconstructing ancestral protein

[tli71193]

Hi there,

I was wondering whether there is a correct way to extract an ancestral reconstructed coding sequence from the 241-mammalian hal file.

So far what I have been doing is say I have the gene sequence for a protein in the human genome <i.e. the gene bed file>. What I have been doing is using halLiftover to find the orthologous gene sequence in say fullTreeAnc115. If I was able to obtain the sequence (most of the time they are fragmented so I just joined them together) I would use minimap2 to align the human coding sequence of the protein to the orthologous gene sequence to get the orthologous coding sequence.

Does this sound correct or would there be issues or more accurate ways to extract the ancestral reconstructed coding sequence? Any feedback would be greatly appreciated!

[diekhans]

Hi Toni, That sounds like a good approach. I might have projected the coding sequence through the alignment between the genome and ancestor. However, I suspect yours will produce very similar results and be more tolerant of alignment errors. Let us know how it works out. Mark Tony Li ***@***.***> writes:

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Hi there, I was wondering whether there is a correct way to extract an ancestral reconstructed **coding** sequence from the 241-mammalian hal file. So far what I have been doing is say I have the **gene** sequence for a protein in the human genome <i.e. the gene bed file>. What I have been doing is using halLiftover to find the orthologous **gene** sequence in say fullTreeAnc115. If I was able to obtain the sequence (most of the time they are fragmented so I just joined them together) I would use minimap2 to align the human **coding** sequence of the protein to the orthologous **gene** sequence to get the orthologous **coding** sequence. Does this sound correct or would there be issues or more accurate ways to extract the ancestral reconstructed **coding** sequence? Any feedback would be greatly appreciated! -- Reply to this email directly or view it on GitHub: #1818 You are receiving this because you are subscribed to this thread. Message ID: ***@***.***>