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Last update on 04. Dec 2013 .
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Weighting of Base Pairings

OCCURRENCE

ARB_NT/ETC/Probe Design/PROBE DESIGN/EXPERT

 

DESCRIPTION

Allows to adjust values indicating the relative strengths of base (mis) pairings. These values are used by ARB_PROBE for the ranking of potential probe target sites.

Define weights:

Type the values to the corresponding subwindows of the 'Relative Strength of Base Pairings' matrix.

Define threshold for splitting melting domains:

Type a value to the 'Threshold for Splitting' subwindow. This value is subtracted from the mean of all pairing values of the potential probe target hybrid. If the resulting value is lower than that of a particular mispairing, it is assumed that the remaining base paired stretches melt independently. The dissociation temperature of the whole hybrid is that of the more stable part of it.

 

NOTES

None

 

EXAMPLES

None

 

WARNINGS

The criteria used for probe target site ranking are based on experimental experience. However, optimum conditions have to be determined experimentally for the particular probe target hybrids.

 

BUGS

No bugs known