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Nucleic Acids Research 2005 33(Web Server Issue):W611-W615; doi:10.1093/nar/gki399
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

OligoWiz 2.0—integrating sequence feature annotation into the design of microarray probes

Rasmus Wernersson* and Henrik Bjørn Nielsen

Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark Building 208, DK-2800, Lyngby, Denmark

*To whom correspondence should be addressed. Tel: +45 45252489; Fax: +45 45931585; Email: raz{at}cbs.dtu.dk

Received February 14, 2005. Revised March 14, 2005. Accepted March 14, 2005.

OligoWiz 2.0 is a powerful tool for microarray probe design that allows for integration of sequence annotation, such as exon/intron structure, untranslated regions (UTRs), transcription start site, etc. In addition to probe selection according to a series of probe quality parameters, cross-hybridization, Tm, position in transcript, probe folding and low-complexity, the program facilitates automatic placement of probes relative to the sequence annotation. The program also supports automatic placement of multiple probes per transcript. Together these facilities make advanced probe design feasible for scientists inexperienced in computerized information management. Furthermore, we show that probes designed using OligoWiz 2.0 give rise to consistent hybridization results (http://www.cbs.dtu.dk/services/OligoWiz2).


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