Generating Genome Projector Views from your genome files

Prerequisite Information:

  1. Installation of G-language System is required in the following steps.
  2. For the handling of genome files with G-language System, see the Introduction to G-language System.

Generating Circular Genome Map View

The function for generating Circular Genome Map View is circular_map(). A folder containing zoomable map with the accession number of given genome as its name will be generated after several minutes.

To generate, simply startup the G-language Shell, load the desired genome, and run the above function as follows:

G > $genome = load("NC_000913.gbk")

Accession Number: NC_000913

  Length of Sequence :   4639675
           A Content :   1142228 (24.62%)
           T Content :   1140970 (24.59%)
           G Content :   1176923 (25.37%)
           C Content :   1179554 (25.42%)
              Others :         0 (0.00%)
          AT Content :    49.21%
          GC Content :    50.79%

G > circular_map($genome)
Map generation will take a few minutes. 
Please make yourself comfortable until the image is generated ;-)

Google Map View is generated in NC_000913 directory.

or by creating a Perl script containing the following code:

use G;
my $genome = load($ARGV[0]);
circular_map($genome);

Generating Genome Map View

The function for generating Genome Map View is genome_map3(). A folder containing zoomable map with the accession number of given genome as its name will be generated after several minutes.

To generate, simply startup the G-language Shell, load the desired genome, and run the above function as follows:

G > $genome = load("NC_000913.gbk")

Accession Number: NC_000913

  Length of Sequence :   4639675
           A Content :   1142228 (24.62%)
           T Content :   1140970 (24.59%)
           G Content :   1176923 (25.37%)
           C Content :   1179554 (25.42%)
              Others :         0 (0.00%)
          AT Content :    49.21%
          GC Content :    50.79%

G > genome_map3($genome)
Image size: 8192 x 8192 pixels.
Using Window size = 4 bp to fit the whole genome...

Map generation will take a few minutes. 
Please make yourself comfortable until the image is generated ;-)

Google Map View is generated in NC_000913 directory.

or by creating a Perl script containing the following code:

use G;
my $genome = load($ARGV[0]);
genome_map3($genome);

Generating DNA Walk Map View

The function for generating DNA Walk Map View is dnawalk(). A folder containing zoomable map with the accession number of given genome as its name will be generated after several minutes.

To generate, simply startup the G-language Shell, load the desired genome, and run the above function as follows:

G > $genome = load("NC_000913.gbk")

Accession Number: NC_000913

  Length of Sequence :   4639675
           A Content :   1142228 (24.62%)
           T Content :   1140970 (24.59%)
           G Content :   1176923 (25.37%)
           C Content :   1179554 (25.42%)
              Others :         0 (0.00%)
          AT Content :    49.21%
          GC Content :    50.79%

G > dnawalk($genome)
Map generation will take a few minutes. 
Please make yourself comfortable until the image is generated ;-)

Google Map View is generated in NC_000913 directory.

or by creating a Perl script containing the following code:

use G;
my $genome = load($ARGV[0]);
dnawalk($genome);

Integrating generated maps to Genome Projector

Following instructions require the local installation of Genome Projector.

Genome Projector folder (minimal version with Escherichia coli genome) contains the following files and folders:

gbt.css			getNodes.cgi*		keggGenome		maps.js
organismlist.txt		gbt.js		index.html*		maps.css
maps.pl*

DNAWalk:
data/		gmap/		hoge.pl		index.cgi*	info.cgi*

GenomeMap:
data/		gmap/		hoge.pl		index.cgi*	info.cgi*	overlay1/

PathwayMap:
data/		gmap/		index.cgi*	info.cgi*	overlay1/

PlasmidMap:
data/		gmap/		hoge.pl		index.cgi*	info.cgi*

images:
apache_pb.gif	macosxlogo.gif	web_share.gif

lib:
adapter/	ext-all.js*	resources/

pict:
block-bg.gif*		menubar.png		searchResults.png

util:
GenomeMapGenerator.pl		OrganismListGenerator.pl	gbt.js.bk
mogrify.pl			selectCircularGenome.pl

Here the four views of Genome Projector are available in four corresponding folders, PlasmidMap(Circular Genome Map), GenomeMap, PathwayMap, and DNAWalk. Each of these folders contain a subfolder named gmap, and this folder contains the custom zoomable views of each of the genomes, with the accession number of the genome as the folder name. Therefore, the custom Genome Projector Views as generated in the above instructions can be directly placed within these gmap folders, and Genome Projector automatically recognizes their availability.

In order to let Genome Projector system know that a new genome is available, you need to edit the organismlist.txt located directly within the GenomeProjector folder. This text file lists the name of organisms with its accession number separated by a “tab”. By adding the name and the accession number of your custom genome activates the newly installed map from the web interface.

Each of the folders of custom views actually contain their own index.html files as with standard custom zoomable maps, so these maps can be viewed independently without Genome Projector.

To implement your own database to these new maps, see this manual.

generating_genome_projector_views_from_your_genome_files.txt · Last modified: 2009/04/19 15:41 (external edit)