Question

Training Genemarkhmm

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12.7 years ago

Daniel Standage 4.1k

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 • 4.6k views

ADD COMMENT • link updated 10.1 years ago by Biostar 20 • written 12.7 years ago by Daniel Standage 4.1k

score 2 · Answer 1 · 2012-03-20

GeneMark is terrific - get the GeneMark-ES program from http://exon.gatech.edu/license_download.cgi (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/gm_es.pl 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.