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

Abstract

The efficiency of molecular methods involving DNA/DNA hybridizations depends on the accurate prediction of the melting temperature ( T_m ) of the duplex. Many softwares are available for T_m 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 T_m . OHM (OligoHeatMap) is an online tool able to provide estimates of T_m 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: T_m 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.