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Nucleic Acids Research Advance Access published online on April 25, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn221
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences

Olivier Croce1,*, François Chevenet2 and Richard Christen1

1University of Nice Sophia-Antipolis and CNRS. UMR 6543, Virtual Biology Lab. Institute of Developmental Biology and Cancer. Parc Valrose. 06108 Nice and 2Genetics and Evolution of Infectious Diseases, UMR 2724 CNRS/IRD-IRD, 911 avenue Agropolis, B.P. 64501, 34394 Montpellier Cedex 5, France

*To whom correspondence should be addressed. Tel: +33 4 92 07 69 47; Fax: +33 4 92 07 69 47; Email: croce{at}unice.fr

Received January 30, 2008. Revised March 28, 2008. Accepted April 10, 2008.

The efficiency of molecular methods involving DNA/DNA hybridizations depends on the accurate prediction of the melting temperature (Tm) of the duplex. Many softwares are available for Tm calculations, but difficulties arise when one wishes to check if a given oligomer (PCR primer or probe) hybridizes well or not on more than a single sequence. Moreover, the presence of mismatches within the duplex is not sufficient to estimate specificity as it does not always significantly decrease the Tm. OHM (OligoHeatMap) is an online tool able to provide estimates of Tm for a set of oligomers and a set of aligned sequences, not only as text files of complete results but also in a graphical way: Tm values are translated into colors and displayed as a heat map image, either stand alone or to be used by softwares such as TreeDyn to be included in a phylogenetic tree. OHM is freely available at http://bioinfo.unice.fr/ohm/, with links to the full source code and online help.


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