What is the best approach to identify TFs in a non-model organism with limited homology to the closest model organism? Is predicting DNA-binding domains and assuming that most proteins containing DBDs are TFs a valid strategy?
Tomas Hessler
This doesn't directly answer your question but have you considered protein clustering with MMseqs2?
An example where it was used to identify homologs across very distantly related organisms: https://www.nature.com/articles/s41586-020-2762-2
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Maximilian Schuff
In deed in case of expected low homology I would focus on TF's Domains. I would suppose that These are still more or less conserved.
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