Recompiling Augustus for short introns

Discussions about predicting genes with AUGUSTUS. Not covered here: WebAUGUSTUS and BRAKER1

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kbseah
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Joined: Wed May 08, 2019 4:58 pm

Recompiling Augustus for short introns

Post by kbseah » Wed May 08, 2019 5:48 pm

Hello everybody,

I'm interested in gene prediction for a genome that we expect to have short introns. I've seen the previous forum post here: http://bioinf.uni-greifswald.de/bioinf/ ... hp?f=5&t=9

However in a paper on the Stentor genome, with short 15 nt introns (doi:10.1016/j.cub.2016.12.057), they describe editing three files in the source code of Augustus v3.0.2: extrinsic.cc, intronmodel.cc, types.cc

Is it still necessary to edit the source code and recompile, as described in that paper?

Thanks, and best regards,
Brandon Seah

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