GraphDNA How-To Information


Load files into DNA Grapher

Load one or more sequences from a local file
Load one or more genome sequences from the VOCS database
Load a gene sequence from the VOCS database

Manipulate the DNA Graph

Switch between skew types
Change the maximum/minimum x and y values
Change the window size

View and navigate the DNA Graph

Use the slider bar at the bottom of the DNA Walker
View genes for one of the genomes in the skew
Export the graph

 

Load one or more sequences from a local file

Go to the File menu and select “Load Sequence from File.” You can load sequences from FASTA, Genbank, or EMBL files; select the appropriate option. A browser window will open in which you can select the file(s) you wish to plot. Note: You will need to upload files one at a time.

Load one or more genome sequences from the VOCS database

First, go to the File menu. You must select a database first, so choose “Change Default Database”. Select a VOCS viral database (e.g. Poxviridae) from the list provided, and click Choose.
Now select “Load Sequence(s) from DB” from the File menu. A list of viral genomes in the selected database will open; select the genomes you wish to load, and click OK. The genomes will load into the graphing window. (Note: this step can at times be slow. Be patient!)

Load gene sequences from the VOCS database

At present, the GraphDNA program is not set up to load individual genes from the VOCS database. However, this is easily enough done by opening VOCS first. Select the Database and open the genomes of interest. Select the genes you wish to graph and, from the Analysis menu, select “DNA Grapher”. A GraphDNA window with the selected genes will automatically open.

Switch between skew types

GraphDNA offers nine skew types:
– purine skew (GC-AT) (vs. residue number)
– keto skew (AC-GT)
– AT skew
– GC skew
– AC skew
– GA skew
– GT skew
– GT skew
– DNA Walker: this graph shows all four nucleotides, each plotted along a different axis.

To switch from one skew type to another, select “Graph Type” from the View menu and click on the type of skew you wish to plot. The graph will automatically update.

Change the maximum/minimum x and y values

Select “Axis Options” from the View menu. Here you can enter new max and min x and y values. Click Apply to regraph with the new parameters. To return the graph to its default values, click Recenter on the bottom left of the GraphDNA console, or select “Recenter” from the View menu.

Change the window size

Window size is a graphing parameter for the DNA skew which governs how much detail is shown. A small window size (10) will mean that the program averages the DNA content over every 10 nucleotides; the resulting graph will have a large amount of small-scale detail. A large window size (200) will average the DNA content over every 200 nucleotides, giving a smoother graph.
The smaller the window size, the longer the graphing process will take. A window size of 70 or more is recommended for larger (dsDNA) genomes.
To change the window size, click in the “Window Size” box in the bottom left-hand corner of the GraphDNA console. Type in the new window size and click “Replot”.

Use the slider bar at the bottom of the DNA Walker

Since DNA Walker is a four-coordinate graph rather than a DNA skew, the graph itself contains no length (residue #) information. The slider bar at the bottom of the GraphDNA console allows you to navigate through the DNA walk by residue number. Slide the bar along; an orange dot will move along the graph from the origin (0, 0) to the end of the DNA walk. The number to the right of the slider bar is the residue number.

View genes for one of the genomes in the skew

GraphDNA allows you to view the top- (red) and bottom- (blue) strand genes in the plotted genomes. Go to the “View Genes for Genome” option in the center of the console; select the genome of interest from the drop-down list. Its genes will appear in the box above, their positions corresponding to the residue number on the x axis of the graph.

Export the graph

GraphDNA offers an automatic export option to png format. Select “Save As” from the File menu. In the browser window that opens, select your file location and name.

 

Tagged with:
 

Comments are closed.