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XHM: A system for detection of potential cross hybridizations in DNA microarrays

Kristian Flikka1*, Fekadu Yadetie23, Astrid Laegreid2 and Inge Jonassen14

Author Affiliations

1 Computational Biology Unit, Bergen Center for Computational Science, UNIFOB/UiB, Thormoehlensgt.55, N-5008 Bergen, Norway

2 Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway

3 Sars International Centre for Marine Molecular Biology, Bergen High Technology Centre, Thormoehlensgt. 55, N-5008 Bergen, Norway

4 Department of Informatics, University of Bergen, PB. 7800, N-5020 Bergen, Norway

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BMC Bioinformatics 2004, 5:117  doi:10.1186/1471-2105-5-117

Published: 27 August 2004



Microarrays have emerged as the preferred platform for high throughput gene expression analysis. Cross-hybridization among genes with high sequence similarities can be a source of error reducing the reliability of DNA microarray results.


We have developed a tool called XHM (cross hybridization on microarrays) for assessment of the reliability of hybridization signals by detecting potential cross-hybridizations on DNA microarrays. This is done by comparing the sequences of the probes against an extensive database representing the transcriptome of the organism in question. XHM is available online at webcite.


Using XHM with its user-adjustable parameters will enable scientists to check their lists of differentially expressed genes from microarray experiments for potential cross-hybridizations. This provides information that may be useful in the validation of the microarray results.