TABLE 2.
Tools and software packages related to finding off-target sites.
| Name | Main functionality | Input | Cell type | Interface | Year | Source |
|---|---|---|---|---|---|---|
| CALITAS Fennell et al. (2021) | CALITAS is a CRISPR-Cas-aware aligner and integrated off-target search algorithm. It supports an unlimited number of mismatches and gaps and allows PAM mismatches or PAM-less searches | gRNA, one or more local regions of a target sequence | Human | Standalone application | 2021 | https://github.com/editasmedicine/calitas |
| CRISPR-SE Li et al. (2021) | It is an accurate and fast search engine using a brute force approach to find all off-target sites | gRNA | Human and mouse genomes | Web user interface | 2021 | The webserver: http://renlab.sdsc.edu/CRISPRSE/ |
| The source code: https://github.com/bil022/CRISPR-SE | ||||||
| CRISPRitz Cancellieri et al. (2020)* | It enumerates and annotates putative off-target sequences and assesses their potential impact on the functional genome. It has three outputs: i) all off-target sites; ii) an overall mismatch and bulge profile for each guide; iii) motif matrices | PAM sequence, a list of guides, References genome (required) and genomic annotations and number of mismatches (optional) | All genome | Standalone application | 2019 | https://github.com/pinellolab/CRISPRitz |
| https://github.com/InfOmics/CRISPRitz | ||||||
| CHOPCHOP v3.0 Labun et al. (2019) | It Identifies sgRNA targets. Five outputs: i) the number of off-targets, ii) whether the off-targets contain mismatches or are perfect hits, and iii) where the target site lies within the gene iv) the results are ranked by GC-content | Four inputs: i) the target; ii) species; iii) CRISPR effector and iv) the purpose of the experiment | 200 genomes | Command-line program and web user interface | 2019 | Server: https://chopchop.cbu.uib.no |
| The local installation: https://bitbucket.org/valenlab/chopchop | ||||||
| CRSeek Dampier et al. (2018) | It finds all on-target and off-target sites | Interested sequence | All genome | Command line interface (Python) | 2018 | https://github.com/DamLabResources/crseek) |
| CRISPR-RT Zhu et al. (2018)* | It retrieves all the protentional targets and relevant information for gRNAs in CRISPR-C2c2 system | An RNA/DNA sequence | 10 genomes include human | Web application | 2017 | http://bioinfolab.miamioh.edu/CRISPR-RT |
| PhytoCRISPEX Rastogi et al. (2016) | It finds potential targets and shows the gene name with start, stop, and sequence of the sgRNA targets. It also shows the results of checks at level one and two | DNA sequences | 13 algae (diatoms, haptophytes, etc.), or any user defined genome | Web interface and UNIX-based standalone application | 2016 | http://www.phytocrispex.biologie.ens.fr/CRISPEx/crispexdownloads/ |
| CRISPResso Pinello et al. (2015)* | It finds potential on and off-targets | Two files for paired-end reads or a single file for single-end reads, and the References amplicon sequence | Any selected genome | Command line interface or web server | 2015 | http://github.com/lucapinello/CRISPResso. Web application www.crispresso.rocks |
| Cas-OFFinder Bae et al. (2014)* | It searches for potential off-target sites and shows their locations, position, direction, and number of mismatches | Genome sequence | Any selected genome | Command line program (written in OpenCL) and website | 2014 | http://www.rgenome.net/cas-offinder |
| CasOT Xiao et al. (2014) | It finds potential off-target sites in any given genome with user-specified types of PAMs, and number of mismatches | target sites or genome and a genome annotation file (optional) | Any selected genome | Command-line program (a Perl script) | 2014 | http://eendb.zfgenetics.org/casot/ |
| COSMID Cradick et al. (2014)* | It retrieves all off-target sites matching the user-supplied criteria in comparison to the guide strand with chromosomal location | The guide sequence, type of PAM, allowed number of mismatches, insertions and deletions, genome of interest, and primer design parameters | 7 genomes including human and mouse | web user interface | 2014 | http://crispr.bme.gatech.edu |
| CRISPRdirect Naito et al. (2015)* | It outputs a list of on and off-target sites with details (target position, target sequence, the number of target sites in the genome, GC content, and calculated melting temperature) | Two inputs: i) an accession number, and ii) a genome coordinate or an arbitrary nucleotide sequence up to 10 kbp | 9 genomes including human and mouse, rat etc. | Web user interface | 2014 | http://crispr.dbcls.jp |
| E-CRISP Heigwer et al. (2014) | It retrieves positions of CRISPR targets | Gene Id or gene sequence | More than 40 genomes | Web user interface | 2014 | http://www.e-crisp.org/E-CRISP |
| GT-Scan O’Brien and BaileyGT-Scan. (2014) | It ranks all potential on and off-targets | Genomic region and target rule (target length, constrained positions and positions with high-, low- or no-target and off-target specificity) | More than 25 genomes | Web user interface | 2014 | http://gt-scan.braembl.org.au |
| sgRNAcas9 Xie et al. (2014)* | It predicts all single or paired CRISPR target sequences and the corresponding information for each target site (such as start and end values, sequence pattern, GC content, sgRNA offset, etc.) | Sequences of target position | All genome | Command line interface (Perl script) | 2014 | www.biootools.com |
| SSFinder Upadhyay and Sharma. (2014)* | It identifies potential off-target sites and classifies them | File name and directory of input sequences | All genome | Command line interface (python) | 2014 | https://code.google.com/p/ssfinder/ |
| CRISPRTarget Biswas et al. (2013) | It predicts the most likely targets of gRNAs. Targets can be displayed and scored for flanking sequences and PAMs | Spacers | Any selected genome | Web application | 2013 | http://bioanalysis.otago.ac.nz/CRISPRTarget |
*Means the tools are free of charge to access.