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Using GALBA for prediction of a specific gene family #58

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panosioannidis opened this issue Nov 28, 2024 · 2 comments
Open

Using GALBA for prediction of a specific gene family #58

panosioannidis opened this issue Nov 28, 2024 · 2 comments

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@panosioannidis
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Can I use GALBA for predicting the genes of a gene family?

Suppose, for example, that I'm interested in finding all cytochrome P450s in a particular species. It would be very nice to be able to give a set of reference P450s (only from the species of interest, or from other species as well) to GALBA and get back a list of P450s in this particular species. The idea is that even though you get most of the P450s using a genome-wide prediction tool such as BRAKER3, there are still some missing (for various reasons: eg not enough RNAseq evidence). Usually, a lot of manual curation is needed in order to obtain all of the genes in a gene family, but this is not scalable (obviously!).

So have you used GALBA for doing such a thing? Or something similar? Or do you know of someone else who has done something similar? And maybe using another approach (i.e. without using GALBA)?

Thanks in advance,
Panos

@KatharinaHoff
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KatharinaHoff commented Nov 28, 2024 via email

@panosioannidis
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panosioannidis commented Nov 28, 2024

Thanks for the response!

Ok, I'll have a look at miniprot... Does it produce a gene model, or just an alignment which I'll then have to convert to a proper gene model (myself)?

I've tried augustus-ppx in the past, but I remember that it needs quite a bit of tweaking and even then it misses some genes. I was hoping for something more automated...

EDIT: just saw that miniprot also produces a gene model as well (with the gff/gtf switch. At least that's what it looks like...

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