TABLE 3.
Tools and software packages related to gRNA design.
| Name | Main functionality | Input | Cell type | Interface | Year | Source |
|---|---|---|---|---|---|---|
| SNP-CRISPR Chen et al. (2020) | It designs gRNAs for non-reference genomes to support allelic targeting. SNP-CRISPR calculates the gRNA efficiency score for the variant and the References sequences | Target genome, variant information including the genome coordinates and sequence changes | Human, Mouse, Zebrafish, Fly | Web application | 2020 | https://www.flyrnai.org/tools/snp_crispr/ |
| AlleleAnalyzer Keough et al. (2019) | It designs allele-specific dual gRNAs. It incorporates single-nucleotide variants and short insertions and deletions to design sgRNAs for precisely editing one or multiple haplotypes of a sequenced genome, currently supporting 11 Cas proteins | Target genome (with genetic variant information) | Human | Application | 2019 | https://github.com/keoughkath/AlleleAnalyzer |
| CRISPR-Local Sun et al. (2019) | It designs sgRNAs in plants and other organisms that factor in genetic variation and is optimized to generate genome-wide sgRNAs | whole-genome sequencing, mRNA sequencing or known variants for specific transgenic receptor lines | Plants | Application | 2018 | http://crispr.hzau.edu.cn/CRISPR-Local/ |
| CRISPR-P Liu et al. (2017)* | It helps to design of gRNA. It output: all targetable sites; the details and GC content of each gRNA; the restriction enzyme site in the targeting region; and synthetic DNA oligos; as well as the microhomology score and the secondary structure of sgRNA. | The gene locus tag, genomic position, or sequence | 49 plant genomes | Web user interface | 2017 | http://cbi.hzau.edu.cn/crispr2/ |
| CRISPR FOCUS Cao et al. (2017)* | It retrieves all possible gRNA and prioritize them. It also provides a rational and high-throughput approach for sgRNA library design | Gene symbols or RefSeq IDs | Human or mouse genome | Web application | 2017 | http://cistrome.org/crispr-focus/ |
| Guide Picker Hough et al. (2017)* | It provides rapid guide RNA generation and selection. It retrieves guide sequences with on and off-target sites | The genome and the gene name | Mouse or human gene | Web application (JavaScript) | 2017 | https://www.deskgen.com/guide-picker/ |
| SgTiler Ahmed and He. (2017)* | It generates graphical representation for distribution of sgRNA. It shows four outputs: i) all candidate sgRNAs; ii) list of filtered sgRNAs; iii) list of sgRNA details; and iv) a summary report with important statistics | Three input files: i) FASTA file; ii) A file with exon coordinates; and iii) a file of regulatory regions | Any selected genome | Command line application (Python) | 2017 | https://github.com/HansenHeLab/sgTiler |
| CRISPOR Concordet and Haeussler. (2018) | It finds guide RNAs in an input sequence and ranks them according to different scores. It evaluates potential off-targets in the genome of interest and predicts on-target activity | A sequence (typically an exon), a genome, and the type of CRISPR nuclease | More than 150 genomes | Web and standalone command line application | 2016 | http://crispor.org |
| CRISPR-DO Ma et al. (2016) | It retrieves information about target sequences, overlaps with exons, putative regulatory sequences and SNPs in the spCas9 CRISPR system | sgRNA | Human, mouse, zebrafish, fly and worm | Web application | 2016 | http://cistrome.org/crispr/ |
| Breaking-Cas Oliveros et al. (2016)* | It retrieves all sequences, coordinates, scores, and annotation details of every gRNA and off-targets | The name of the References organism, the characteristics of the Cas-like nuclease, and the sequence(s) of the intended target genomic | All eukaryotic genomes | Web application | 2016 | http://bioinfogp.cnb.csic.es/tools/breakingcas |
| CT-Finder Zhu et al. (2016) | It helps users to design gRNAs optimized for specificity and shows Graphic visualization of on and off-target sites in Cas9n and RFNs | DNA sequence, a References genome, the on and off-target PAM sequences, and length of gRNA and seed region | Human, mouse, Arabidops | Web application | 2016 | http://bioinfolab.miamioh.edu/ct-finder |
| CRISPETa Pulido-Quetglas et al. (2017) | It helps to design sgRNAs | One or more target regions | Human, mouse, zebrafish, Drosophila, melanogaster and Caenorhabditis elegans | Command-line and web application | 2016 | Server: http://crispeta.crg.eu/manual Source code: https://github.com/guigolab/CRISPETA |
| CLD Heigwer et al. (2016)* | It helps to design sgRNAs | Three files: i) the genome sequence, ii) a parameter (Hwang and Bae, 2021) file, and iii) a gene list | All organisms | Command line application | 2016 | htts://github.com/ |
| CRISPy-web Blin et al. (2016)* | It scans for gRNAs and potential off-targets | Target sequence or gene | Any microbial genome | Web application | 2016 | http://crispy.secondarymetabolites.org |
| EuPaGDT Peng and Tarleton. (2015) | It finds all gRNAs. It also scores, and ranks them. Additionally, it assists users in designing single-stranded oligonucleotides for homology-directed repair | Sequence or gene | Eukaryotic organisms | Web application | 2015 | http://grna.ctegd.uga.edu |
| Spacer Scoring for CRISPR(SSC) Xu et al. (2015)* | It predicts SgRNA efficiency | DNA sequence | Any selected genome | Web application | 2015 | http://crispr.dfci.harvard.edu/SSC/ |
| Cas-Designer Park et al. (2015)* | It aids researchers in choosing appropriate target sites in a gene of interest. It outputs a list of all possible gRNAs and their potential off-target sites, including bulge-type sites, and also an out-of-frame score for each | DNA sequence | Most of genomes (Wang et al. (2019a) | Command line interface | 2015 | http://rgenome.net/cas-designer/ |
| CRISPR multitargeter Prykhozhij et al. (2015) | It searches input sequences for single-sgRNA and two-sgRNA/Cas9 nickase targeting | sgRNA, GC% | 12 genomes like zebrafish | Web application | 2015 | http://www.multicrispr.net/ |
| CRISPR-ERA Liu et al. (2015)* | It designs gRNA. It outputs sgRNAs, on and off target location, and details of them with their E- and S-scores etc. | Target gene or genomic site | 9 common prokaryotic and eukaryotic organisms | Web application | 2015 | http://crisprera.stanford.edu/InitAction.action |
| CCTop Stemmer et al. (2015)* | It identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation | Target genome site | 15 common prokaryotic and eukaryotic organisms | application (python) | 2015 | http://crispr.cos.uniheidelberg.de/ |
| CRISPRseek Zhu et al. (2014)* | It identifies gRNAs and also scores and ranks them to minimize off-target cleavage | Any sequence | Any selected genome | Command line application ® | 2014 | http://www.bioconductor.org |
*Means the tools are free of charge to access.