EffectorP 3.0?

[bob100077]

Are there any plans to introduce EffectorP 3.0 - fungi to the pipeline?
I know this version is fairly recent.

Thanks!
Chris Bonner

PS. Thank you so much for putting this together, it's been a total pain working between them, especially with dependencies and installations.

Sperschneider J and Dodds PN (2021) EffectorP 3.0: prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes. MPMI. Abstract

[darcyabjones]

Hi Chris!

Yes it's always been harder than it should be.
I hope the pipeline helps, but of course I only really hear from people when things go wrong so it's hard to gauge :).

The latest versions of the pipeline do run EffectorP 3 already.
It isn't incorporated into the ML ranking method yet (i'm currently working on an update to include it) but the results are in the tables.

I haven't included the "fungi" mode though if that's what you mean.
From what I remember reading there wasn't really any benefit to excluding the oomycete model when classifying fungal effectors.
I'll benchmark the "fungi" mode and see whether I should include it as a separate column as I've done for deepredeff.

Happy to hear suggestions or thoughts :)

[bob100077]

Great!
Again, thank you so much for all of your hard work putting these into a user friendly pipeline!