Project Overview
MitoEdit is a bioinformatics tool designed to facilitate targeted base editing in DNA sequences, with a particular focus on mitochondrial DNA editing. The tool implements various editing pipelines based on published research, allowing researchers to identify optimal target windows for specific base conversions.
MitoEdit analyzes DNA sequences to predict target windows for base editing using different editing systems, identifies potential bystander edits, and provides optimal TALE (Transcription Activator-Like Effector) sequences for targeting.
Editing Pipelines
MitoEdit implements the following editing pipelines:
1. Mok2020 G1333
Purpose: Predicts target windows for C.G-to-T.A conversions in a 5'-TC context using the G1333 DddA split.
This pipeline identifies 5'-TCs on both DNA strands and generates target windows (14-18bp) with editable cytosines at positions 4-10bp from the 5' end.
2. Mok2020 G1397
Purpose: Predicts target windows for C.G-to-T.A conversions in a 5'-TC context using the G1397 DddA split.
This pipeline identifies 5'-TCs on both DNA strands and generates target windows (14-18bp) with target cytosines at positions 4-7bp from the 3' end.
3. Mok2022 G1397 DddA11
Purpose: Predicts target windows for C.G-to-T.A conversions in a 5'-HC context (where H = A, C or T) using the modified DddA domain (DddA11).
This pipeline identifies 5'-HCs on both DNA strands and generates target windows (14-18bp) with target cytosines at positions 4-7bp from the 3' end.
4. Cho sTALEDs
Purpose: Predicts target windows for A.T-to-G.C conversions in a 5'-AS or 5'-SA context (where S = C or G) using the AD domain.
This pipeline identifies 5'-SA and 5'-AS contexts on both DNA strands and generates target windows (14-18bp) with target adenines at positions 5-12bp from the end to which the AD domain is tethered.