Explanation of values, fields and graphics presented in the tool.
Cleavage %
The 3' cleavage distribution of each PAS is shown as a blue bar chart. The values (Cleavage %) are non-normalized (they do not sum to 100%). Rather, Cleavage % is scaled with respect to the strength of the PAS relative to the average affinity of a distal, well-separated PAS.
Isoform Window
The window frame shown on top of the cleavage distribution defines what cleavage positions define the isoform of interest. All isoform metrics are calculated by aggregating the cleavage within this window.
Isoform Score
The aggregate APA isoform log odds ('strength') of the wildtype sequence, with respect to the average affinity of a well-separated, distal PAS. The histogram to the right shows the distribution of native human pA sites and their isoform scores. This metric is an unbiased estimate of the overall affinity (strength) of the PAS sequence, in relation to all other possible PAS configurations.
Instructions
Instructions on how to use the tool.
Choose model and configuration
Select the generative model to use for sampling new pA sequences. The user is free to choose both the model architecture and the pA dataset it has been trained on. Also specify how many sequences to generate. Press the Generate-button to sample the sequences.
Inspect sequences
The generated sequences are displayed in a table. Click on a sequence to load it into the cleavage distribution plotting tool.
Define isoform window
Drag the tabs of the isoform window over the region of the cleavage distribution according to what pA positions you wish to include in the isoform of interest.
Zoom and pan the sequence
Zoom and pan into specific regions of the sequence by pressing the zoom buttons above the cleavage curve, or simply by scrolling and dragging with the mouse over the cleavage curve.