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

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W154-6. doi: 10.1093/nar/gkn221. Epub 2008 Apr 25.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Graphics
  • Internet
  • Nucleic Acid Denaturation
  • Nucleic Acid Hybridization
  • Oligonucleotide Probes / chemistry*
  • Polymerase Chain Reaction
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Software*
  • Thermodynamics

Substances

  • Oligonucleotide Probes