Gene Information PagesΒΆ


  1. Download the file and unzip into plugins directory.
  2. Edit database details in services/settings.php file.
  3. Edit the conf.json file, if needed to display sequence information inside the gene pages.


Navigate to http://[your server name]/genie/gene?id=[gene id] or http://[your server name]/genie/transcript?id=[transcript id]

Sequence informationSequences will be displayed under the sequence tab once we configure the config.json file.

Sequence coloring

Following script will be used to load genome gff3 file into corresponding sequence coloring table(sequence_color) in GenIE database. This feature will be shaded the genomic,transcriptomic and cds sequence regions in gene information pages.

#get the gene.gff3 file and loaded into database table calles sequence_color
#Usage: sh /data/Egrandis_297_v2.0.gene.gff3

awk '/mRNA/{split($2,a,"=");sub(/ID=./,a[2]";");print $1;next}/gene/{;next}{sub(/ID=./,a[2]";");print $1}' FS=\; OFS=\; $1 | awk '!/#/{print $9"\t"$1"\t"$3"\t"$4"\t"$5}' > tmp &&
sed -i 's/five_prime_UTR/5UTR/' tmp && sed -i 's/three_prime_UTR/3UTR/' tmp  &&
/usr/bin/mysql --host=localhost --user=[user] --password=[pass] --local_infile=1 --database=egrandis<<EOFMYSQL
TRUNCATE TABLE  sequence_color;
LOAD DATA LOCAL INFILE "tmp" INTO TABLE sequence_color fields terminated by '\t' LINES TERMINATED BY '\n' ignore 0 lines;
rm tmp