Synthetics RSS Explorer

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To examine how each base in an RSS contributes the dynamics of recombination, we selected an endogenous sequence (V4-57-1) to serve as a reference sequence and systematically made point mutations across the heptamer, spacer, and nonamer regions and examined their behavior. In the plots below, the behavior of the reference sequence is shown in grey with a chosen point mutation in bright blue. The heatmaps show the effect of each mutation with respect to the reference sequence, with a green hue indicating a decrease and a purple hue representing an increase in the corresponding property. Glyphs with a yellow circle in front designate the original nucleotide in that position of the reference sequence. A cross (x) represents a mutation that wasn’t studied.

To examine the looping frequency, dwell time distribution, and posterior probability of the cleavage probability, click on a point mutation in the heatmap. The selected point mutation will be highlighted in all three heatmaps and the distributions will be plotted in blue. Pressing ESC on your keyboard will clear your selection and clicking the “Reset” button will clear the plots back to only the reference state.

This figure was created using the Bokeh plotting library. The code used to generate this figure can be found on the code page of this website. An offline version of the figure can be downloaded here.