Logo Plot | Sequence Bar Plot | Sequence Activity Relationship | SARvision
Using Sequence Logo and Bar Plots to Study Sequence Activity Relationships
by Mark Hansen, Ph.D.
A logo plot highlights residues that are important by scaling font size with activity.
A Logo plot is a common way to summarize sequence motifs that display some biological function. These sequence logos take the form of stacked letters that are bounded by a rectangle, or bar, scaled in height relative to their frequency in a data-set or to some aggregate activity. The Y-axis controls the activity field and method used in height scaling. There are two Chart styles, Sequence Logo and Sequence Bars: the Sequence logo performs statistics based on a basis set of 20 natural amino acids to scale font size, while the Sequence Bar plot scales based on data so that an arbitrary number of monomers can be used for scaling. As such the Sequence logo option should be used only with protein and peptides built using only a natural amino acid basis set. Note the Color scheme is an option to recolor the plot by any of the predefined residue color schemes. The Filter residues checkbox control filters out residues from the plot. This can be useful for analyzing alanine scan information.
A sequence logo plot can display sequence motifs that define a biological activity.
The Bar label option can alter the display from using actual letters to drawing solid rectangular bars (instead of a bounded letter) with the letter code drawn as a label on each. The height of the bar corresponds to the aggregate activity for each residue displayed at each position. Because a single bar contains many sequences, an aggregate of the of the Y-axis values is used to calculate Y-axis height (average, min or max).
The Sequence bar plot can be displayed as letters or solid bars. The Y-axis can be counts or any data field modified and aggregated by average, min or max.
Hovering with the mouse on any sequence position in the logo plot spawns a bar-plot displaying that positions data as a second bar plot: each monomer is plotted along the X-axis. These carts are useful to identify bars that are too small to make out on the main plot. These pop up charts can be copied to the clip board or saved to file to use in reports.
Fly overs slice the chart by position to show a plot of each residue at that position.
Finally, logo plots can be created on subsets of data. Using a subset filter and the Filter by option (top left), logo plots can be built on demand by changing the definition of activity in the Subset range filters (left). In the example below, a logo plot is created using only sequences that are active against the SST1 receptor (<350nM) and inactive against the SST4 receptor (>100nM) as defined in Subset 1. This is an attractive way to display motifs representing varying activity profiles.
Using a subset filter, logo plots can be built t represent specific activity profiles.