What is state-of-the-art for orthology inference? Anything in the works we should be watching for? Have been using orthofinder2 and most interested in maximizing accuracy and number of genes with calls (not computation speed). Methods incorporating alpha-fold predictions? Synteny/collinearity? - ThreadSky

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samyeaman.bsky.social • 36 days ago

What is state-of-the-art for orthology inference? Anything in the works we should be watching for? Have been using orthofinder2 and most interested in maximizing accuracy and number of genes with calls (not computation speed). Methods incorporating alpha-fold predictions? Synteny/collinearity?

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jssantangelo.bsky.social•36 days ago

GENESPACE incorporates synteny information and works well for identifying orthologs. Runs Orthofinder and MCScanX under the hood.

https://github.com/jtlovell/GENESPACE

mtanichthys.bsky.social•36 days ago

Haven't seen Alphafold used in orthology prediction but for sure there are a handful of methods incorporating synteny/collinearity. I don't think there's a top dog here yet, but pSONIC is one I've heard of. Unfortunately haven't gotten a chance to try it yet. https://academic.oup.com/g3journal/article/11/8/jkab170/6275219

conjustover.bsky.social•36 days ago

If you get the change to try it, any and all feedback would be appreciated!

mtanichthys.bsky.social•36 days ago

I think an alternative "state-of-the-art" are the approaches that combine annotation and orthology determination, usually adopting a comparative approach. A couple years old review here:
https://www.annualreviews.org/content/journals/10.1146/annurev-animal-020518-115005

But, TOGA is a new player in this game: https://www.science.org/doi/full/10.1126/science.abn3107

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