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What is seDNA

seDNA is a Java Applet which searches for residues whose conservation is higher than a certain threshold. You can choose that threshold.

Designed by Mirabela RUSU.

How to use seDNA

   Input file:

seDNA uses msf files generated by ClustalW.

   Output file:

The output file starts with the name of the input file (alignment file), the name of the output file and the options used by the applet.

The result of the seDNA search is shown below the ClustalW alignment. Only the residues whose conservation is above the threshold are shown.

Symbols:

• "~"  conservation is below threshold
• "*"  the columns do not contain a valid symbol: a residue or a gap (-)

Trouble using seDNA

If you have troubles using seDNA, it might be because you didn’t accept the certificate which appeared on the screen when the page loaded. The solution is to quit you browser and reopen the page and trust this applet.

If the message:

 « Your browser does not support Java, so nothing is displayed. »

 appears, or nothing loads at the top of the page and no message is displayed , or nothing happens after clicking, that means that you should install Java Virtual Machine.

 You can get the latest Java VM at http://java.sun.com/j2se/1.4.2/download.html. You have to get the JRE that is appopriate for your platform.

If, during the installation, you are given an option to use the new Java VM with your browser, make sure that you do set up the Java VM to work with your browser.

For Mac OS X, Java comes with the operating system. For Mac OS 8 or 9, you need to get the Macintosh Runtime for Java (MRJ) 2.2.5 at http://developer.apple.com/java/download.html

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