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Find below the detailed description of each graph. Note that cha= racters A, C, G and T in the formulas denote the number of corresponding nu= cleotide in a window.
DNA Flexibility =E2=80=94 searches for r=
egions of high DNA helix flexibility in a DNA sequence. The average
(sum of = flexibility angles in the window) / (the window size - 1)=20
For more= detailed information see = DNA Flexibility paragraph.
GC Content (%) =E2=80=94 shows the perce= ntage 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=20
AG Content (%) =E2=80=94 shows the perce= ntage of nitrogenous bases (either adenine or guanine) on a DNA molecule. I= t is calculated by the following formula:
(A+G)/(A= +G+C+T)*100=20
GC Deviation (G-C)/(G+C) =E2=80=94 shows= the difference between the =E2=80=9CG=E2=80=9D content of the forward stra= nd and the reverse strand. GC Deviation&nb= sp;is calculated by the following formula:
(G-C)/(G= +C)=20
AT Deviation (A-T)/(A+T) =E2=80=94 shows= the difference between the =E2=80=9CA=E2=80=9D content of the forward stra= nd and the reverse strand. AT Deviation&nb= sp;is calculated by the following formula:
(A-T)/(A= +T)=20
Karlin Signature Difference =E2=80=94 di= nucleotide absolute relative abundance difference between the whole sequenc= e and a sliding window. Let:
f(XY) = =3D frequency of the dinucleotide XY f(X) =3D frequency of the nucleotide X p(XY) =3D f(XY) / f(X) * f(Y) p_seq(XY) =3D p(XY) for the whole sequence p_win(XY) =3D p(XY) for a window=20
The Karlin =
Signature Difference for a window is calculated by=
the following formula:
sum(p_se= q(XY) - p_win(XY)) / 16=20
Informational Entropy =E2=80=94 is calcu= lated from a table of overlapping DNA triplet frequencies. The use of overl= apping triplets smooths the frame effect. Infor= mational Entropy is calculated by the following formula:
-(triple= t frequency)*log10(triplet frequency)/log10(2)=20