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

BMC Bioinformatics

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

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]	–

ISSN: 1471-2105