Table 2.
Base editing tools comparative table
| Tool | BE-FF | BE-Designer (20) | beditor (21) | Benchling (https://www.benchling.com/) | BEable-GPS (22) |
|---|---|---|---|---|---|
| BE varietiesa | 17 CBEs and 9 ABEs | Limited (3 CBEs, 1 ABE) | 12 CBEs and 8 ABEs | Limited (CBEs only) | Limited (only CBEs) |
| Customized user defined BE support | Support customized deaminase type, PAM, activity window and gRNA orientation | Support customized deaminase type and activity window. Limited to predefined PAMs and their gRNA orientations | Support customized deaminase type as well as hypothetical BEs, PAM, activity window and gRNA orientation | Support customized PAMs. Customized activity window or deaminase not supported | Support customized PAM, activity window, gRNA orientation and length. Limited to CBEs only |
| Identify suitable BEs to correct specific point mutations | V | X | X | X | V (limited to CBEs) |
| Translate editing outcome and detect synonymous corrections | V | V | X | V | X |
| Identify the BEs for correcting the outcome of a transversion mutation | V | X | X | X | X |
| User interface | Webserver | Webserver | GUI or command line (requires installation). Limited OS support | Integrated as a feature on the Benchling web interface | Webserver |
| Support multiple SNVs analysis | V | V | V | X | X |
| Off-targets assessment | V (limited to NGG-based BEs) | V | V | V (limited to NGG-based CBEs) | X |
| Targeting approach | • Detects suitable BEs to reverse a given SNV. • Can be utilized for designing base editing-mediated therapeutics, or generating point mutations |
Shows the predicted base-editing outcome for a given sequence by a user-defined BE | Shows the predicted base editing outcome for a given sequence by a user-defined BE | Shows the potential gRNAs for a user-defined DNA region within a sequence file and presents the editing outcome for the pre-defined BE. | Target region can be specified. Shows the base editing outcome of selected BEs |
| Input format | • Fetch by SNP ID • Fetch by genomic coordinates of diverse genomes • Multiple SNVs file • Standard input by user |
• Multiple SNVs file • Standard input by user |
Multiple SNVs file. Requires several parameters including genome, coordinates, transcript id, ref and var values for DNA and AA | DNA sequence file | Standard input by user |
aBase editors with the same properties are counted as a single base editor. e.g. BE1, BE2, BE3, HF-BE3, BE4(max) and BE4-Gam share the same parameters and therefore considered as the same BE