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Table 4 Tools available for sgRNA designing

From: CRISPR/Cas9: the Jedi against the dark empire of diseases

Tool

Website

Purpose

Input

Output

Available genomes

Pros

Cons

Reference

Atum

https://www.atum.bio/eCommerce/cas9/input

Candidate gRNA

DNA sequence, (max 10,000 bp) gene name, genomic region

Candidate guidesequences and off target loci

5

Uses ATUM scoring to minimize off-targets/all in one nickase ninja

Not free of cost

N/A

Benchling

https://benchling.com/crispr

Candidate gRNA

DNA sequence/gene name

Candidate guidesequences and off target loci

5

Free of cost

 

N/A

CRISPR design

http://crispr.mit.edu/

Used to find target sequences for a sequence or seuqnces (batch mode), also provides in depth on/off target information

DNA sequence/FASTA files single or batch mode

Candidate guide sequences and off target loci

16

Helpful to generate many candidates with on/off information

Only handles short sequences up to23–500 bp/slow to use/no efficacy merit/does not indicate identity of mismatches

[39]

CHOPCHOP

https://chopchop.rc.fas.harvard.edu/

To find target sequences for a single sequence/gene/transcript

DNA sequence/gene name/genome location

Candidate guide sequences and off target loci,

23

Good to generate multiple guides for a single target, free of cost

No on-target efficacy

[40]

Cas off finder

http://www.rgenome.net/cas-offinder/

Provides information about OTs without limiting the PAM or number of mismatch bases

sgRNA

Off target loci for guide sequences

20

Free of cost/easy to use

Does not give indication if OTs are in coding sequences

[41]

Fly CRISPR

http://tools.flycrispr.molbio.wisc.edu/targetFinder/

Candidiate gRNA, software provides maximum stringency-(uses strict algorithm based on OT cleavage in cells lines) and minimum stringency; off target cleavage effects observed

DNA sequence

Candidate guidesequences and off target loci,

18

Free of cost

Slow to use

[42]

E-CRISP

http://www.e-crisp.org/E-CRISP/designcrispr.html

Finds target sequences for a single gene or sequence

DNA sequence/gene symbol

Candidate guide sequences and off target loci,

30

Free of cost

Numerous options maybe confusing/no account for identity of mismatches

[43]

Cas OT

http://eendb.zfgenetics.org/casot/

To find potential off targets in any genome

FASTA files

sgRNA and OT sites

User input

Free of cost/ First tool that identifies off-targetes in a user specified genome

No account for identitiy of mismatches

N/A

CRISPR ERA

http://crispr-era.stanford.edu/

Used for genome wide screening based on CRISPR, CRISPRi and CRISPRa

DNA sequence, gene name or TSS location

Candidate guide sequences and distances to TSS

9

Free of cost/can also be used for genome imaging and CRISPR synthetic circuit design

 

[44]

CCTop

http://crispr.cos.uni-heidelberg.de/

It helps in identifying and ranking all sgRNA targets sites according to off target quality

DNA sequence/FASTA file single/batch/ sequences 23 to 500 bp

Scores OTs and also ranks sgRNA by OTs

45

Free of cost/easy to use

No on–target efficacy prediction

[45]

WU-CRISPR

http://crispr.wustl.edu/

Potential candidate gRNA

DNA sequence/gene symbol

sgRNA list ranked by efficacy score

2 (Human and mouse)

Free of cost/easy to use

No account of identity of mismatches

[46]

GTscan

http://gt-scan.csiro.au/

Used to find target sequences and OTs for a single sequence

DNA sequence/FASTA file

SgRNA, genomic sites with 0 to 3 mismatches

51

Free of cost/easy to use

Trouble in finding exact matches in genome

[47]

CRISPR direct

https://crispr.dbcls.jp/

To find target sequences for a single transcript/sequence

DNA sequence/genome location/transcript

Target sequence and position

20

Free of cost/rapid visual display of target sequence and OT information

No on-target efficacy

[48]

COD

http://cas9.wicp.net/

Used to find target sequences for an input sequence

DNA sequence up to 400 bp

Gene bank file/CSC file/ OT scoring

27

Free of cost/easy to use/ OT scoring

Slow to use/no on-taget prediction

N/A

sgRNA scorer 2.0

https://crispr.med.harvard.edu/

Used to find target sequences/OT using Casfinder

DNA sequence/FASTA files upto10 kb

Target sequence with activity score

14

Free of cost/ allows to identify target sites for any CRISPR system

Slow to use/OT prediction does not account identity

N/A

CRISPOR

http://crispor.tefor.net/

To find candidate guide sequences

DNA sequence 1000 bp

Guide sequence with specificity score/guides for OTs

146

Free of cost

N/A

[49]