Purdue University

genemark

Link to section 'Introduction' of 'genemark' Introduction

GeneMark-ES/ET/EP contains GeneMark-ES, GeneMark-ET and GeneMark-EP+ algorithms.

Link to section 'Versions' of 'genemark' Versions

• 4.68
• 4.69

Link to section 'Commands' of 'genemark' Commands

• bed_to_gff.pl
• bp_seq_select.pl
• build_mod.pl
• calc_introns_from_gtf.pl
• change_path_in_perl_scripts.pl
• compare_intervals_exact.pl
• gc_distr.pl
• get_below_gc.pl
• get_sequence_from_GTF.pl
• gmes_petap.pl
• hc_exons2hints.pl
• histogram.pl
• make_nt_freq_mat.pl
• parse_ET.pl
• parse_by_introns.pl
• parse_gibbs.pl
• parse_set.pl
• predict_genes.pl
• reformat_gff.pl
• rescale_gff.pl
• rnaseq_introns_to_gff.pl
• run_es.pl
• run_hmm_pbs.pl
• scan_for_bp.pl
• star_to_gff.pl
• verify_evidence_gmhmm.pl

Link to section 'Academic license' of 'genemark' Academic license

Go to the GeneMark web site: http://exon.gatech.edu/GeneMark/license_download.cgi. Check the boxes for GeneMark-ES/ET/EP ver 4.69_lic and LINUX 64 next to it, fill out the form, then click "I agree". In the next page, right click and copy the link addresses for 64 bit licenss. Paste the link addresses in the commands below:

cd $HOME
wget "replace with license URL"
zcat gm_key_64.gz > .gm_key

Link to section 'Module' of 'genemark' Module

You can load the modules by:

module load biocontainers
module load genemark/4.68 

Link to section 'Example job' of 'genemark' Example job

To run GeneMark on our cluster:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=genemark
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers genemark/4.68  

gmes_petap.pl --ES  --cores 24 --sequence scaffolds.fasta