Find below the detailed description of each graph. Note that characters A, C, G and T in the formulas denote the number of corresponding nucleotide in a window.
DNA Flexibility — searches for regions of high DNA helix flexibility in a DNA sequence. The average Threshold in a window is calculated by the following formula:
(sum of flexibility angles in the window) / (the window size - 1) |
For more detailed information see DNA Flexibility paragraph.
GC Content (%) — shows the percentage of nitrogenous bases (either guanine or cytosine) on a DNA molecule. It is calculated by the following formula:
(G+C)/(A+G+C+T)*100 |
AG Content (%) — shows the percentage of nitrogenous bases (either adenine or guanine) on a DNA molecule. It is calculated by the following formula:
(A+G)/(A+G+C+T)*100 |
GC Deviation (G-C)/(G+C) — shows the difference between the “G” content of the forward strand and the reverse strand. GC Deviation is calculated by the following formula:
(G-C)/(G+C) |
AT Deviation (A-T)/(A+T) — shows the difference between the “A” content of the forward strand and the reverse strand. AT Deviation is calculated by the following formula:
(A-T)/(A+T) |
Karlin Signature Difference — dinucleotide absolute relative abundance difference between the whole sequence and a sliding window. Let:
f(XY) = frequency of the dinucleotide XY f(X) = frequency of the nucleotide X p(XY) = f(XY) / f(X) * f(Y) p_seq(XY) = p(XY) for the whole sequence p_win(XY) = p(XY) for a window |
The Karlin Signature Difference for a window is calculated by the following formula:
sum(p_seq(XY) - p_win(XY)) / 16 |
Informational Entropy — is calculated from a table of overlapping DNA triplet frequencies. The use of overlapping triplets smooths the frame effect. Informational Entropy is calculated by the following formula:
-(triplet frequency)*log10(triplet frequency)/log10(2) |