Web/based exercises

Visualisation of DNA Structures in Complete Genomes
Cookbook

BACKGROUND

1. Handy "Pedestrian guide to Unix" for the CBS Ph.D. course. This is a good place to go for brushing up on basic commands, such as how to view, edit, and print files in Unix.
   
   
2. For more information about the structural parameters used in Atlases, see the DNA Structural Atlas Background page. For more details about methods and applications, have a look at the Atlas REFERENCES page.

What you need to start

All you need is a DNA sequence file, in your directory, preferably in either GenBank or FASTA format, although of course it is possible to convert from other formats.

You can use your own sequence file, if you would like. (You can download a GenBank file, using the "getgene" command, if you know the GenBank accession number for your sequence.) As a sample file, you can download the GenBank file for an E. coli O157 pathogenicity plasmid, and name it "Ecoli_pO157.gbk" by using the following command:

getgene AB011549 > Ecoli_pO157.gbk

Make the GeneWiz postscript (.ps) files.

The postscript files are made by using the "gmake" command. For example, to make the Genomeatlas for the Ecoli_pO157.gbk file, you would type the following:

gmake Ecoli_pO157.genomeatlas.ps

NOTE:

For this exercise, there are seven different possible GeneWiz atlases you can make:

1. Base Atlas (Ecoli_pO157.baseatlas.ps), which is an analysis of the base composition of the genome.



2. Repeats Atlas (Ecoli_pO157.repeatatlas.ps), which plots the global and local repeats throughout the genome.



3. Structure Atlas (Ecoli_pO157.structureatlas.ps), which looks at various types of DNA helical properties within the genome.



4. Genome Atlas (Ecoli_pO157.genomeatlas.ps), which is a combination of the best of each of the above atlases, and is a good overview of the genome.



5. Cruciform Atlas (Ecoli_pO157.cruciformatlas.ps), which localises regions of palindromic symmetry.



6. A-DNA Atlas (Ecoli_pO157.ADNAatlas.ps), which looks for purine stretches (likely to form A-DNA).



7. Z-DNA Atlas (Ecoli_pO157.ZDNAatlas.ps), which looks for alternating pur/pyr stretches (which might form Z-DNA).

For more information about the atlases, see lecture notes from the Ph.D. course.

View your results

You can use ghostview to see the .ps file you've created.

For example, to view the Genomeatlas for the Ecoli_pO157.gbk file, you would type the following:

ghostview Ecoli_pO157.genomeatlas.ps

To print the file on the colour printer, mark the atlas page, and use the "print marked pages" option from the ghostview programme. When prompted for the printer, type the following command:

xerox

Now all you have to do is to analyse the results and figure out what it all means!

For those of you who are interested in more details . . .

You can make (and modify) configuration files (*.cf) for the atlases. For example, suppose you were interested in the DNA structural atlas file for the pO157 genome. You could make the configuration file (gmake Ecoli_pO157.structureatlas.cf), and then edit it (using your favourite editor - for example: nedit Ecoli_pO157.structureatlas.cf ). You can change the order of the wheels, as well as the colour and scaling, or add new wheels.

Link to the DNA Genome Atlas page.

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Last modified on: 31 Oktober, 2001 by Dave Ussery