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URL:
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http://bioinfo.unice.fr/ohm/
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What you can do:
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An online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences.
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Highlights:
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- 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.
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Keywords:
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- oligomers
- DNA hybridization
- oligonucleotides
- DNA melting temperature
- T(m)
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Literature and Tutorials:
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PubMed Link: OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences
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