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Description Hands On Lab Exercises for Artemis
Related-course materials Structural annotation with MAKER Structural annotation with EGN-EP
Authors Stéphanie Bocs (
Lucile Soler (
Jacques Dainat (
Creation Date 26/09/2018
Last Modified Date 27/09/2018


Goal of the exercise

Install & configure artemis :

Download Artemis from (e.g. v17 20180928).

Increase the memory allocated to Artemis following the FAQ recommendations For instance -Xmx8g (Java max heap size) instead of -Xmx2g in Artemis.cfg if you have 16Gb of RAM on your personal computer

Get annotation and evidence gff3 files :

To facilitate manual annotation, match_part must be linked in Artemis, so gff files need to be reformatted. For your information, from the Eugene-EP IFB appliance:

awk 'BEGIN{g=0}{if($3 ~ /EST_match/){g++; print $1"\t"$2"\tgene\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\tID="g; print  $1"\t"$2"\tmRNA\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9";Parent="g}else{if($3 ~ /match_part/){print $0}else{print $0}}}' Chr4.est1.gff3 |sed  's/match_part/exon/' > Chr4.est1_gene.gff3

Reformatted data are centralised on the Slovenian VM, for your information MAKER formatting

awk 'BEGIN{g=0}{if($3 ~ /protein_match/){g++; print $1"\t"$2"\tgene\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\tID="g; print  $1"\t"$2"\tmRNA\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9";Parent="g}else{if($3 ~ /match_part/){print $0}else{print $0}}}' protein_gff\:protein2genome.gff |sed  's/match_part/CDS/' > protein2genome_gene.gff
awk 'BEGIN{g=0}{if($3 ~ /^match$/){g++; print $1"\t"$2"\tgene\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\tID="g; print  $1"\t"$2"\tmRNA\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9";Parent="g}else{if($3 ~ /match_part/){print $0}else{print $0}}}' augustus_masked.gff |sed  's/match_part/exon/' > augustus_masked_gene.gff

Transfer the reformatted annotation files from the Slovenian VM to your personal computer

scp -r -P 65034 .
scp -r -P 65034 .

Launch artemis & Load data :






Some Artemis functionalities :

Annotate AT4G32500 :

Annotate AT4G32510 :

mRNA complement(15685903..15688811)

CDS complement(join(15685903..15686359,15686452..15686777,15686908..15686994,15687072..15687167,15687259..15687432,15687523..15687689,15687772..15687937,15688025..15688163,15688258..15688450,15688544..15688626,15688708..15688811))