To search for regions of high DNA helix flexibility in a DNA sequence, open the sequence in the Sequence View and select the Analyze ‣ Find high DNA flexibility regions item in the context menu. Note that only standard DNA alphabet is supported, i.e. the sequence should consist of characters A, C, G, T and N.
The following dialog appears:
The calculation is made for overlapping windows along a given sequence. If there are two or more consecutive windows with an average flexibility threshold (in each window) greater than the specified Threshold parameter, such area is marked by an annotation.
The average threshold in a window is calculated by the following formula:
(average window threshold) = (sum of flexibility angles in the window) / (the window size - 1)
The following flexibility angles are used during the calculation:
| Dinucleotide | Angle | Dinucleotide | Angle |
|---|---|---|---|
| AA | 7.6 | CA | 14.6 |
| AC | 10.9 | CC | 7.2 |
| AG | 8.8 | CG | 11.1 |
| AT | 12.5 | CT | 8.8 |
| GA | 8.2 | TA | 25 |
| GC | 8.9 | TC | 8.2 |
| GG | 7.2 | TG | 14.6 |
| GT | 10.9 | TT | 7.6 |
A minimum value is used when N characters is present in a dinucleotide:
- CN, NC, GN, NG, NN: 7.2
- AN, NA, TN, NT : 7.6