[maker-devel] gene predictors in MARKER

[Carson Holt]

The gene predictors have to be trained first, and when they are trained
they produce an HMM file that can be supplied to MAKER.  You can either
use MAKER's protein2genome option or est2genome option to produce rough
models to train with, or you can try one of the models that come
prepackaged with those algorithms.

SNAP models will be in --> /sw/maker/2.10/bin/../exe/snap/HMM
Augustus --> run this to see species in augustus -->
/sw/maker/2.10/bin/../exe/augustus/bin/augustus --species=help
GeneMark is self training.  Run it one directly on your genome fasta or
for speed just a chromosome or two of the assembly and it will produce a
file called es.mod as part of it's results.  That is the file you need.

If you have any questions or issues with training just let us know.

Thanks,
Carson



On 12-04-17 7:22 PM, "Huanle" <elzedliu at gmail.com> wrote:

>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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