Sequence comparision with dotplot

dotplot is used with compare to plot areas of similarity between two sequences.

Configuring GCG to plot with telnet

1. Log on to your GCG account and start GCG

2. Configure plotting

To use dotplot you must use a telnet emulator with TEK emulation (i.e., "Better Telnet"), or else use either the GCG X-windows or web interface. If you use Better Telnet, be sure that TEK emulation is turned on under the menu "favorites/edit favorites." Use the "terminal" tab to set TEK emulation to 4105.

GCG will have to be set to where you want to have plots set. First copy the file ".gcgmydevices" into your home directory. This only needs to be done the first time you use your account to plot.

>cp /users/bsci348s/.gcgmydevices .

Set plotting with setplot. This has to be done at the beginning of every GCG session, but only once per session.

>setplot

You will be presented with a menu, with the option "plot-telne" highlighted. If it is not highlighted, use the cursor keys to highlight it, then press "return" to accept this setting.

If you prefer, you can use setplot to send graphical output to a postscript file (simply use the arrow keys to highlight that option and press return). The postscript file can be sent to a postscript printer, either directly from the GCG platform, or indirectly by transferring the file (using ftp) to a desktop computer which is attached to a postscript printer.

Creating a dotplot

1. Read the dotplot help page

>genhelp dotplot

2. Create a working directory called "plt" and use cd (change directories) to make that your current working directory

>mkdir plt

>cd plt

3. Download the files containing the sequences you want to compare.

In this example both of the sequences are swissprot files; they are the same seqeunces that are used in the figure showing dotplot in your textbook. You can also use fetch to retrrieve genbank files. The computer "umbi" has a local copy of genbank installed on it, and the sequences are retrieved from this database. Because the UMBI database is not updated as often as the NCBI database, if you use the web interface to find files at NCBI, you may need to copy the files in another way.

>netfetch p00748

>netfetch p00750

These files will be copied into your current working directory, and will be given the extension ".swissprot", so they will appear as "p00748.swissprot" and "p00750.swissprot."

4. Use compare to generate a datafile (give the filename an extension ".dat"). There are two ways to do this:

1. Allow compare to prompt you for parameters
2. Use the command line syntax

While you are learning GCG you will probably find it easier to have the program prompt you for parameters. As you become more comfortable with GCG you may prefer to use the command line syntax.

Command line syntax:

>compare p00748.swissprot p00750.swissprot -out=comparison.pnt -default

This will compare the sequences in the two data files, and will write a new file called "comparison.pnt." The "-default" argument tells compare to use the default settings for all other options. Be sure that you understand the default parameters before you use this or you may have unexpected results!

5. Plot the datafile with dotplot

If you have not yet set your account to plot with telnet (above), do so now.

>dotplot comparision.pnt -default

A TEK window should appear on your screen, and should create a dotplot that resembles the one in your textbook. This window can be resized by using your mouse to drag the lower right corner of the TEK window.

Additional resources:

Dotplot used for visualizing comparisons among a variety of things http://www.research.att.com/~jon/dotplot/

Dottyplot, a stand alone program (mac OS) for dot-plotting is available at the IUBIO archive: http://iubio.bio.indiana.edu/soft/molbio/mac/

Text: Baxevanis and Oullette (1998). Bioinformatics, Wiley Interscience, page 149.