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Gaius-Augustus / GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.
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Protein.fa files #28

Closed zhoudreames closed 1 year ago

zhoudreames commented 1 year ago

I have no-human genome（pig）, and I want to do gene annotation for it. but I don't know how to choose the protein files, Should I only choose a pig protein file or can I combine multiple species. Thanks~

KatharinaHoff commented 1 year ago

I recommend to choose 4 or more protein sets (e.g. pig, human, mouse, … and maybe goat or cow or even both). Concatenate the files, simplify headers.

We have previously looked into pig. Sus scrofa has a decent annotation.

It is important to repeat mask the genome, first.

zhoudreames @.***> schrieb am Di. 11. Apr. 2023 um 02:57:

I have no-human genome（pig）, and I want to do gene annotation for it. but I don't know how to choose the protein files, Should I only choose a pig protein file or can I combine multiple species. Thanks~

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zhoudreames commented 1 year ago

We have previously looked into pig. Sus scrofa has a decent annotation

Thank you for your detail response， I try it.