[maker-devel] gene predictors in MARKER

Huanle elzedliu at gmail.com
Tue Apr 17 17:22:53 MDT 2012


I am using MAKER to annotate a recently assembled plant genome.
Hi There,

I am using MAKER to annotate a recently assembled plant genome.

I followed the tutorial here: http://gmod.org/wiki/MAKER_Tutorial

The denovo gene predictors i included in the maker_exe.ctl file are
#-----Ab-initio Gene Prediction Algorithms
snap=/sw/maker/2.10/bin/../exe/snap/snap #location of snap executable
gmhmme3=/sw/GeneMark/20120203/bin/gmhmme3 #location of eukaryotic
genemark executable
gmhmmp= #location of prokaryotic genemark executable
augustus=/sw/maker/2.10/bin/../exe/augustus/bin/augustus #location of
augustus executable

However, I am not sure whether they were really used.

During the running, i could see repeatmasker, exonerate and wublast
were called. But i did see any information popped up for those gene
predictors.

So i am wondering if they were actually used.

Could you please let me know how to know if all or one of those gene
predictors were called by marker?

Kind Regards,
Huanle




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