Can Orthofinder accept whole genome data?
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3.0 years ago

I'm planning to use Orthofinder to scan for orthologous groups across a set of genes in snakes. I'm working with whole genome data. I realize Orthofinder requires proteomic data as input. Before I attempt to transform my genomic data into proteomic data, I wanted to check if there is a way to by-pass this? Have any recent updates enabled Orthofinder to accept whole genome data as input?

Thank you for your help!


Orthofinder Whole Genome Orthologous • 1.3k views
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I think you are having trouble with a few concepts here.

  • there is no easy transforming of genomic data to proteomic data. The process is called genome annotation and is not something to take lightly (your species has some influence here)
  • since you are taking about genes in snakes , you thus already have a gene set (=the genome annotation result). What do you mean with 'genomic data' then? coordinates on a genomic sequence?
  • OrthoFInder works with proteins for several different reason (will not go into detail here). In a non-advisable approach you could also feed it with gene (DNA) blast results.

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