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wu-lab-egio / EGIO

Exon Group Ideogram based detection of Orthologous exons and Orthologous isoforms
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How to prepare orthologous genes in non-model species #6

Closed Tang-pro closed 1 week ago

Tang-pro commented 2 months ago

Hi, @wu-lab-egio

There is no species I am studying in Inparanoid. I use OrthoFinder to identify orthologous genes. Here I need a protein sequence, but should I choose the protein sequence corresponding to the longest transcript? Or is there any other method?

Best!

wu-lab-egio commented 2 months ago

Hi,

According to previous studies, you can use protein sequence of the longest transcript as input.

Tang-pro commented 2 months ago

Hi, @wu-lab-egio

But this seems a bit troublesome. First, extract the longest protein sequence to replace the gene, and then identify the orthologous isoform through orthologous gene. I would like to ask if there is any way to identify the orthologous gene directly from gene-level without using the protein sequence?

wu-lab-egio commented 2 months ago

Protein sequence is still required to generate orthologous gene pairs. For example, two genes might share similar sequence, but they might have great changes in peptide sequence by a single nucleaotide reading frame shift mutation.