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OligoWiz 2 Server

This server performs intelligent design of oligonucleotides for DNA microarrays.

IMPORTANT UPDATE (August 2013): Make sure to download the GUI client version 2.3.0 (or better) - it fixes the connection problems we have had over the summer.

Graphs and oligo selections
Example screenshot form the client program

Instructions Article abstract Databases

[Previous version: OligoWiz 1.0]


A detailed protocol for using OligoWiz has recently be published in Nature Protocols:

Rasmus Wernersson, Agnieszka S. Junkcer and Henrik Bjørn Nielsen
Probe selection for DNA microarrays using OligoWiz
Nat Protoc. 2007;2(11):2677-91

If you don't have access to Nature Protocols you can request a reprint (PDF) by emailing to this address:


OligoWiz 2.0 is implemented as a client-server solution, which consist of an easy to use Graphical User Interface (written in Java) which delegates the computationally intensive operations to a powerful Multi-CPU server hosted at the Center for Biological Sequence Analysis.

All the user needs to do is to download and start the GUI.


Current release

Starting with version 2.2.0 the OligoWiz GUI requires Java 1.5 (or newer - version 1.6 is recommended).

Current version: v.2.3.0 (August , 2013) - view changes.

Note: in some browsers you may have to right click and choose "Save Target As...". Also, some browsers have been reported to rename the OligoWiz-2.x.x.jar file to *.zip. If this happens the file must be re-rename to *.jar.

Older releases

Releases prior to version 2.2.0 can run on Java 1.4 (or newer - Java 1.5 / 1.6 will work fine).

Browse all releases (also useful if you encounter a problem with the newest version).


If Java is allready installed, starting the OligoWiz 2.0 client is as easy as double-clicking the file (Windows and MacOS X).

For UNIX systems the application must be started from the command prompt:

java -jar OligoWiz-2.2.0.jar
(or similar for newer versions).

Out of Memory!

If you run large sets of sequences on OligoWiz 2.0 you may experience memory problems. In most cases this can be fixed by executing OligoWiz 2.0 in the following way (in a prompt): java -jar -Xmx300m OligoWiz-2.jar Where "300m" is the maximum amount of memory allocated by OligoWiz-2.jar (300 megabytes)

HTTP proxy:

In order to set up OligoWiz 2.0 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).


If your computer doesn't alway have Java installed - a suitable version of Java (version 1.5 or newer) can be downloaded here:

  • for most computing platforms, including Windows
The OligoWiz 2.0 client can be used free of charge for both academic and commercial use, in combination with the OligoWiz 2.0 server hosted at CBS. However, please see the access policies of the CBS server.


20 Yeast genes with introns

Sampe dataset in TAB format with both sequence and annotation of intron/exon structure: [67 kb]

This dataset was created from GenBank files, using the FeatureExtract server.

270 Yeast genes with introns

Sampe dataset in TAB format with both sequence and annotation of intron/exon structure: [1470 kb]

This dataset was created from GenBank files, using the FeatureExtract server, a comprehensive description of the file format is found here.

30 Bacillus genes

FASTA (sequence only - no annotation) file containing 30 Bacillus subtilis coding regions.
datasets/B.subtilis.30.cds.fsa [17 kb]
[Taxonomy: Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus. ]


For publication of results, please cite:

OligoWiz 2.0 - integrating sequence feature annotation into design of microarray probes
Rasmus Wernersson and Henrik Bjørn Nielsen.
Nucleic Acids Research, 2005, Vol. 33, Web Server issue W611-W615

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

ISMB 2005 software demo

All files related to the demo of OligoWiz 2.0 at ISMB 2005 can be found here: ISMB2005 files

Link to the OligoWiz 2.0 demo at the ISMB 2005 software demo webpage.

Rasmus Wernersson, personal webpage:


Would you prefer to run OligoWiz at your own site? The client part of OligoWiz 2.0 is available as a stand-alone software package, with the same functionality as the service above. There is a download page for academic users; other users are requested to contact CBS Software Package Manager at

Notice: The development of the OligoWiz client (the Java program) is more rapid than the OligoWiz server package. Starting with OligoWiz version 2.1.0 all versions of the OligoWiz client is also build in an OFFLINE version, which can be used together with in command-line version of OligoWiz. Please see the all releases directory.


Scientific and technical problems: