The Graph Menus

ACT has two menus that control which graphs/plots are displayed along side the sequences. Some general information about the graphs can be found in the section called Graphs and Plots.

The Graphs(top) Menu

The items in this menu controls the graphs for the top sequence.

The Graphs(bottom) Menu

The items in this menu controls the graphs for the bottom sequence.

GC Content (%)

Controls whether the GC content plot is visible. This is a graph of the average GC content of a moving window (default size 120 base), across the bases visible in the overview window. [Default: off] [short name: gc_content]

GC Content (%) With 2.5 SD Cutoff

Controls whether the cutoff GC content plot is visible. This is similar to the GC content graph, but the plot is clipped so that the GC content of each algorithm window is shown only when it is more than 2.5 times the standard deviation of the GC content in all the windows. [Default: off] [short name: sd_gc_content]

AG Content (%)

Controls whether the AG content plot is visible. This is a graph of the average AG content of a moving window (default size 120 base), across the bases visible in the overview window. [Default: off] [short name: ag_content]

GC Frame Plot

Controls whether the GC frame plot is visible. This graph is similar to the GC content graph but shows the GC content of the first, second and third position independently. For more information on the algorithm and on how to interpret the result see this web page. [Default: off] [short name: gc_frame]

Correlation Scores

Controls whether the (forward) correlation scores plot is visible. The graph shows the correlation between the amino acid composition of the globular proteins in TREMBL and the composition of the base translation in each of the three reading frames. The green line represents forward frame 1, blue represents frame 2 and red represents frame 3. [Default: off] [short name: correlation_score]

Reverse Correlation Scores

This does the same as "Correlation Scores", but does the calculation on the reverse strand. The green line represents reverse frame 1 (the bottom frame line), blue represents frame 2 and red represents frame 3. [Default: off] [short name: correlation_score]

GC Deviation (G-C)/(G+C)

Controls whether the GC deviation plot is visible. This graph shows the difference between the "G" content of the forward strand and the reverse strand. [Default: off] [short name: gc_deviation]

AT Deviation (A-T)/(A+T)

Controls whether the AT deviation plot is visible. This graph shows the difference between the "A" content of the forward strand and the reverse strand. [Default: off] [short name: at_deviation]