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Table 1 Comparison table between PnB Designer and other guide RNA design applications

From: PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants

Tool PnB Designer SNP-CRISPR BE-FF beditor BE-Designer Benchling
pegRNA design for prime editing  ×   ×   ×   ×   × 
Protospacer design for prime editing  ×   ×   ×   × 
Integrated PAM variants for ABE 7 0 6 6 6 0
Assessment of off-targets  × 
Support multiple sample file import  ×   × 
Explanatory feedback after wrong input  ×   × 
Guide design on non-reference genome  ×   ×   × 
Access Webserver Webserver Webserver Installation in python environment and GUI or command line Webserver Integrated feature on the benchling website
Input format Genomic coordinates, text format sequence input by user Genomic coordinates file only SNP ID, genomic coordinates, text format sequence input by user Genomic coordinates file only Genomic coordinates file, text format sequence input by the user DNA sequence on the benchling website
URL fgcz-shiny.uzh.ch/PnBDesigner/ flyrnai.org/tools/snp_crispr danioffenlab.com/be-ff pypi.org/project/beditor rgenome.net/be-designer/ benchling.com
Reference Chen et al. [38] Rabinowitz et al. [18] Dandage et al. [19] Hwang et al. [20]