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Using braker for small open reading frame prediction
Posted: Thu Jul 13, 2017 5:48 pm
Hello, I am currently trying to identify small open reading frames and was hoping to be able to use augustus/braker to do so. I am able to alter the minimum gene size within genemark-et but do not know how to focus on intergenic regions if I wish to do so or to reduce the gene size for augustus. I am using the braker.pl version 1.9 and augustus 3.2.3. Thank you
Re: Using braker for small open reading frame prediction
Posted: Tue Jul 25, 2017 9:00 am
AUGUSTUS can in principle find small open reading frames. It is not an easy task, though.
There is a parameter /Constant/min_coding_len that you can set to a shorter length (default is 201). You find that parameter in the species_parameters.cfg file for your species. However, this will probably not lead to the result you are looking for. You would also need to alter the exon length distribution in species_exon_probs.pbl of your species to create a probability to detect such short genes.
This currently requires editing species parameter files. It is not something that BRAKER1 will do automatically.