pre-compiled datasets

Discussions about training AUGUSTUS from various sources of evidence. Not discussed here: BRAKER1 and WebAUGUSTUS!

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lucas.schmitz
Posts: 2
Joined: Sun Aug 27, 2017 8:55 pm

pre-compiled datasets

Postby lucas.schmitz » Sun Aug 27, 2017 9:04 pm

I have a question about the config files for the built-in species. What was the general strategy to generate/train these? I.e. did it involve high quality genbank files, genome contigs, RNAseq, proteome, ESTs, or a combination of these? I'm curious what would be the ideal data to train Augustus as viewed by the developers. Also, is there anyway I could retrace this in the Augustus installation? I tried to find metadata or something similar to no avail.

lucas.schmitz
Posts: 2
Joined: Sun Aug 27, 2017 8:55 pm

Re: pre-compiled datasets

Postby lucas.schmitz » Sun Aug 27, 2017 9:21 pm

just a quick follow-up: in the 2004 paper by Mario Stanke "AUGUSTUS: a web server for gene finding in eukaryotes" I read that single-gene training sets were used to estimate parameters. So, what exactly are these single-gene training sets? Are these highly accurate/manually curated genes not necessarily from the same organism?


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