[maker-devel] Maker with Augustus

[david.swarbreck]

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