Question: Training Genemarkhmm
gravatar for Daniel Standage
8.3 years ago by
Daniel Standage3.9k
Davis, California, USA
Daniel Standage3.9k wrote:

I am preparing to annotate the genome of a non-model organism using Maker. As part of its pipeline, Maker runs GeneMarkHMM. Can I train a model specifically for this genome to improve the predictions generated by GeneMarkHMM. The documentation does not seem to be clear on this.

gene genome training • 3.4k views
ADD COMMENTlink modified 5.8 years ago by Biostar ♦♦ 20 • written 8.3 years ago by Daniel Standage3.9k
gravatar for Sujai Kumar
8.3 years ago by
Sujai Kumar240
United Kingdom
Sujai Kumar240 wrote:

GeneMark is terrific - get the GeneMark-ES program from (my file was called gm_es_bp_linux64_v2.3e.tar.gz). Follow the instructions for installing it.

Once done, run:

../gm_es_bp_linux64_v2.3e/gmes/ DraftGenome.fasta --min_contig 20000 >logfile

It will create a whole bunch of folders in the cwd. The HMM file that you provide to MAKER is in mod/es.mod

Hope this helps.

ADD COMMENTlink written 8.3 years ago by Sujai Kumar240
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