The Graphs tab enables you to display a range of additional metrics on your sequences. The type of graphs which are available depend on the type of sequence you are viewing, and are listed in the sections below. For information on alignment graphs, see section 9.3.2 . The number control to the right of each graph controls the height of that graph (in pixels).
Sliding window size. Many types of graph use a sliding window when calculating values. This calculates the value of the graph at each position by averaging across a number of surrounding positions. When the value is 1, no averaging is performed. When the value is 3, the value of the graph is the average of the residue value at that position and the values on either side.
GC content. This plots a graph of the GC content of the sequence within a window of speciﬁed length as the window is moved along the sequence. If Frame Plot is checked, the graph shows the GC content in the 3rd codon position only for each frame, where frame 1 = red, frame 2 = green and frame 3 = blue.
Chromatogram. This is available with chromatogram traces, and displays the chromatogram trace above the sequence. If Qual is checked the quality scores are displayed as a blue graph overlaid on the chromatogram. For more information on viewing chromatograms, see section 5.6 .
Stylized DNA Helix. Shows the bases in your sequence as a rotating DNA helix. To turn oﬀ the rotation, uncheck the “Animated” option.
Amino Acid Charge. This runs the EMBOSS charge tool to plot a graph of the charges of the amino acids within a window of speciﬁed length as the window is moved along the sequence.
Hydrophobicity. This displays the Hydrophobicity of the residue at every position, or the average Hydrophobicity when there are multiple sequences.
pI. pI stands for Isoelectric point and refers to the pH at which a molecule carries no net electrical charge. The pI plot displays the pI of the protein at every position along the sequence, or the average pI when multiple sequences are being viewed. The values in this graph are normalised such that the amino acid with the lowest PI has a value of 0, and the amino acid with the highest PI has a value of 1, and all other amino acid’s values are interpolated linearly according to their PI.