[maker-devel] Question about "maker-", "augustus_masked", "snap_masked" gene model

[Carson Holt]

MAKER uses all derived models as a pool of alternate models for a given locus.  The one that best matches the aligned evidence is then selected using the AED calculation described in the MAKER2 publication. Overall hint based models tend to perform better than the raw models because they get extra info about observed intron/exon structure from alignments. There is also a discussion of this in the MAKER2 paper.

—Carson



> On Sep 18, 2017, at 9:07 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Hello:
> 
> Would you please explain what is the difference between "maker-...-agustus..." and "augustus_masked..." gene models? 
> 
> I know  "augustus_masked..." gene models are raw august predictions, while "maker-...-agustus..." are hit derived gene models. But by default, maker2 reports gene models with evidence support (protein sequences or transcripts). Then why some gene models are hit derived while other models (with evidence support) are raw augustus prediction (even there are protein sequences or transcript evidence)?
> 
> BTW, is it true that generally the "maker-...-agustus..." gene models are more reliable than the "augustus_masked..." gene models?  
> 
> Thanks
> 
> Best
> Quanwei