[maker-devel] Maker with Augustus

[Carson Holt]

Sorry for the slower than average response.  My wife went into labor over the weekend.

For the initial training of augustus, you can either select an existing organism or do the training yourself.  Once augustus is trained, MAKER will produce both the ab initio gene predictions (without hints) and hint based predictions for you.  You don't have to worry about building the hints file.  MAKER does that for you based on alignments produced from the EST and protein evidence you provided in the maker_opts.ctl file.  Just make sure you set the AUGUSTUS_CONFIG_PATH environmental variable in your profile per the augustus install instructions.

I hope that answers your question.  If not let me know.

Thanks,
Carson


On 10/15/09 12:29 PM, "david.swarbreck" <dswarbreck at stanford.edu> wrote:

Hi,

I have a question relating to using Augustus as the predictor with
Maker. From looking at the documentation for augustus the hints files
detailing aligned features uses a non-standard GFF format. These include
the use of non SO compliant features such as exonpart (treated
differently to exon by augustus) and the inclusion of a source
identifier in col9 which has to be specified in the augustus config. In
addition in the standalone Augustus setting a bonus and penalty is
required for obeying a hint feature.

So my question is when using Augustus as the predictor in Maker is Maker
taking care of this for me or do i still need to define exonparts as
distinct from exon and provide bonus and penalty information. Is there a
particular GFF3 format which maker requires to define for example
alignments e.g can these use the match type (e.g. EST_match), can this
use the cigar format or should these features be described as exons.

Any help appreciated
david


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