ab initio prediction of non-canonical splice sites

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

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swarbred
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Joined: Thu Sep 02, 2021 1:07 pm

ab initio prediction of non-canonical splice sites

Post by swarbred »

We are annotating species where we anticipate a substantial percentage of non-canonical splicing e.g. ga-ag I wondered if there were any updates to augustus to support ab intio prediction of splice sites outside of gt-ag and gc-ag. I'm aware there is support for annotating non-canonical sites via hints e.g. viewtopic.php?f=5&t=124&p=490&hilit=canonical#p490

Other groups have made there own edits e.g. https://github.com/chancx/dinoflag-alt-splice but I wanted to see if there was any recent / future changes that would support this.
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