non-canonical splice site patterns

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

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katharina
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non-canonical splice site patterns

Post by katharina »

Originally posted in the old forum by Bram on 26.10.2012 - 12:56
I would like to adopt Augustus into my prediction pipeline but I need to inquire into one issue: Can Augustus handle non-canonical splice sites except (except for AT-AC)?
The species I work on have GT-TG, GC-CG,... and more. If I provide these things as intron hints, will Augustus accept it? Or will it force the gene structure into GT/GC-AG?
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katharina
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Re: non-canonical splice site patterns

Post by katharina »

by Mario on 26.10.2012 - 12:58
The option

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--allow_hinted_splicesites=gttg,gccg
allows Augustus to predict these introns in addition to the GT-AG and GC-AG introns that are allowed by default. However, it will not predict these ab initio only. It will predict only those non-standard introns that are supported by hints, e.g. from spliced RNA-seq reads.
You may also want to have a look at the bottom of this readme:
http://bioinf.uni-greifswald.de/augustu ... naseq.html
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