Institute of Bioinformatics Münster

Gene Structure Draw FAQ

Each line has two parts:
  1. name of the gene: string (without any white space, colon) e.g. geneA
  2. exon-intron structure:
    • a single exon starting at location 20 and ending at location 30 is represented by the string 20:30
    • if there are multiple exons, the individual exon strings are separated by commas e.g. 20:30,50:70,90:120
Each gene is specified on a single line with the name, structure separated by a space.
geneA 10:20,50:60,80:200
geneB 60:80,90:150
The gene is assumed to start at location 1. The length of the gene is assumed to be the maximum endpoint of any of its exons. The length can also be set explicitly. If the gene with label geneA has length 1000bp, it can be represented by the string geneA:1000. If you want to depict only some exons of a gene but want to have the length proportional to the actual length, you may want to use this feature.
geneA:300 10:20,50:60,80:200
geneB:500 60:80,90:150
Yes. Start the line with #.
Each domain needs to be assigned a color and a unique name. To represent the domain dom1 in blue color include at the top the following line.
#color dom1 0 0 255
The location of the domain e.g. 15:85 on the gene is given after the exon-intron structure and a semicolon. Multiple domains can be specified as shown below:
#color dom1 0 0 255
#color dom2 0 255 0
geneA 10:20,50:60,80:200;15:85:dom1,100:150:dom2
The color code is a r(red), g(green), b(blue) triplet in which each of the components can be set to a number between 0 and 255 (inclusive). Lower values lead to dark colors and higher values to lighter colors. Here are some useful combinations:
  • (0,0,0) black
  • (255,255,255) white
  • (255,0,0) red
  • (0,255,0) green
  • (0,0,255) blue
Yes. Exons can be given labels. Exons in adjacent genes structures that have the same label are joined in the manner dictated by the options (line/polygon).
#color dom1 0 255 0
#color dom2 255 0 0
geneA:300 10:20:E1,50:60,80:200;100:150:dom1
geneB:200 60:80:E1,90:150:E1;70:120:dom2
geneC 20:70:E1,120:190;30:40:dom1,60:150:dom2
As you can see there are a large number of options that can be set for this script. The cookie merely remembers the options that you choose - this may be handy if you are a frequent user of the site. We have neither the time/necessity/expertise necessary to track anyone :) Still you can always refuse/delete the cookie through your browser tools...
2012-11-20 10:33