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Using GALBA for prediction of a specific gene family #58
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You are looking for something like AUGUSTUS-PPX, but miniprot will be
easier to use.
panosioannidis ***@***.***> schrieb am Do. 28. Nov. 2024 um
12:07:
… 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
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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 |
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
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