[maker-devel] Possible ways to improve annotated gene numbers

[Carson Holt]

MAKER excludes models without evidence support (this is because gene predictors can overcall by as much as a factor of 10, i.e. lots of false positives). So you may be lacking in either protein or transcript evidence (you should alway supply a minimum of 2 related proteomes for any MAKER analysis - transcript evidence by itself is insufficient).

You can also try and rescue models based on protein domain content using iprscan. Details in this protocol paper —> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/>

—Carson
 



> On Jun 30, 2017, at 1:30 PM, Qihua Liang <qlian003 at ucr.edu> wrote:
> 
> Dear Maker Development Team,
> 
> Hi, I am using Maker for annotation and BUSCO to evaluate the completeness. 
> 
> For de novo perditions, I am using Augustus, GeneMark, and SNAP, and the annotated proteins have completeness of ~80%, ~50%, ~50% correspondingly. When I cat all de novo annotated proteins of these three tools, the completeness is much higher as ~92%. 
> 
> But for all.maker.proteins.fasta, the completeness is only ~80%.
> 
> 1. Does this mean that some proteins annotated by Augustus/GeneMark/SNAP, are not included in the file all.maker.proteins.fasta? Does it because such excluded proteins do not have hits with the EST evidences?
> 
> 2. To achieve a higher BUSCO completeness, what possible ways can be used? Including more EST evidences from other species?
> 
> 
> Thank you
> Qihua
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