DNA Flexibility

To search for regions of high DNA helix flexibility in a DNA sequence:

1. Open the sequence in the Sequence View.
2. Right-click and select Analyze → Find high DNA flexibility regions.

🧬 Note: Only the standard DNA alphabet is supported: A, C, G, T, and N.

Settings Dialog

The following dialog appears:

Method

The analysis uses a sliding window approach. For each window:

• If 2 or more consecutive windows have average flexibility above the threshold, the region is annotated.
• The average flexibility for a window is calculated as:

Average = (Sum of dinucleotide flexibility angles in the window) / (window size - 1)

Flexibility Angles Table

Handling Unknown Bases (N)

If the sequence contains an ambiguous base N, the following minimum angle values are used:

• CN, NC, GN, NG, NN → 7.2
• AN, NA, TN, NT → 7.6

• Configuring Dialog Settings
• Result Annotations