Hi all,

I have a dataset from a base editing experiment where some spacers show efficient editing, while others show little or no editing. In addition, among the edited sites, some show the intended conversion (e.g. A to G), whereas others show unintended or “mis-editing” events (e.g. A to C or A to T).

I would like to identify sequence patterns or motifs in the flanking regions that may explain:

• Why certain target bases are more prone to editing than others
• Why some targets undergo correct editing versus incorrect base
  conversions

Specifically, I am interested in approaches to analyze the local sequence context (e.g. 1-3 bp around the edited base) to discover motifs associated with:

• High vs low editing efficiency
• Correct (A to G) vs incorrect edits

Has anyone worked on similar analyses, or can recommend computational/statistical methods or tools (e.g. motif discovery, k-mer enrichment, ML approaches) that are suitable for this type of problem?

Any suggestions or references would be greatly appreciated.