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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]