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<H3><A NAME="SECTION00050300000000000000">
Thermodynamic model for inosine computation</A>
</H3>
<P>
If it is possible, you directly can create a new class which extends the InosineNNMethod class
(melting.patternModels.wobble).
<BR>
<BR>
The InosineNNMethod class already implements the following public functions of the PatternComputationMethod interface.:
<SPAN CLASS="textit">ThermoResult computeThermodynamics(NucleotidSequences sequences,int pos1, int pos2, ThermoResult result)</SPAN>,
and <SPAN CLASS="textit">isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)</SPAN>.
<BR>
<BR>
An InosineNNMethod can compute the enthalpy and entropy of a Crick's pair containing an inosine base by adding
the thermodynamic parameters for each Crick's pair containing an inosine base.
The implemented function <SPAN CLASS="textit">isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)</SPAN>
can determine if a thermodynamic parameter for one of the Crick's pair containing an inosine base is missing.
<BR>
<BR>
Finally, the implemented function <SPAN CLASS="textit">int[] correctPositions(int pos1, int pos2, int duplexLength)</SPAN> is necessary
to take into account the adjacent base pairs of the base pair containing the inosine.
<P>
<BR><HR>
<ADDRESS>
Computational Neurobiology
2009-08-24
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