Note: OligoWiz2.0 has been released

OligoWiz 1.0 Server

This server performs intelligent design of oligonucleotides for DNA microarrays.

OligoWiz is implemented as a client-server solution, which consist of an easy to use Graphical User Interface (the client - written in Java) which delegates the computationally intensive operations to a server (which by default is hosted at CBS on a powerfull Multi-CPU SGI UNIX server). All the user needs to do is to download and start the GUI.

The client is written in Java 1.3.1 with portability in mind. It is tested on MacOS X, Linux and Windows, but should work on any platform with Java 1.3.1 or better. The client communicates with server using the HTTP protocol.

Graphs and oligo selections
Example screenshot form the client program

Instructions Article abstract Databases


New version: v.1.0.8 (9th of April , 2003) - view changes.

The most recent version of the OligoWiz client can be downloaded here as a Java Archive (JAR).
Note: for some browsers you may have to right click and choose "Save Target As..."
Also, some browsers have been reported to rename the OligoWiz.jar file to *.zip. If this happens the file must be re-rename to *.jar.

Browse all releases.

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Running OligoWiz

If Java is allready installed, starting the OligoWiz client is as easy as double-clicking the file (Windows and MacOS X), or typing java -jar OligoWiz.jar at the command prompt (Unix).

Out of Memory! If you run large sets of sequences on OligoWiz you may experience memory problems. In most cases this can be fixed by executing OligoWiz in the following way (in a prompt): java -jar -Xmx300m OligoWiz.jar Where "300m" is the maximum amount of memory allocated by OligoWiz.jar (300 megabytes)

HTTP proxy: In order to set up OligoWiz to access our server through a proxy, the proxy parameters need to be parsed to the JVM on the command prompt: java -jar -Dhttp.proxyHost=proxyhost -Dhttp.proxyPort=portNumber OligoWiz.jar (Put in you relevant proxyhost/port number).

Java: A suitable version of Java (choose J2SE version 1.3.1 or newer) can be downloaded here:

The OligoWiz client can be used free of charge for both academic and commercial use, in combination with the OligoWiz server hosted at CBS. However, please see the access policies of the CBS server.


The sample input data set is a FASTA file containing 30 Bacillus subtilis coding regions. It can be used as a test input for the OligoWiz client program.


For publication of results, please cite:

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.
Henrik Bjørn Nielsen, Rasmus Wernersson and Steen Knudsen.
Nucleic Acids Research, 2003, Vol. 31, No. 13 3491-3496


Would you prefer to run the OligoWiz server at your own site? OligoWiz 1.0 server is available as a package on a commercial license. Send inquiries by e-mail to


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