CRISPR/Cas tools: Difference between revisions
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This page contains a list of tools designed for CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated nucleases) target prediction. CRISPR is a genome engineering mechanism bacteria use to defend against DNA damage. The tools are presented on a table along with some of their key features.
| Tool Name | Searches whole genome for targets | Returns all targets of genome | Seed span and location can be defined | Maximum number of mismatches supported | Available Protospacer adjacent motif (PAM) sequences | Annotation is reported | gRNA suggestion or scoring | External Link | References |
|---|---|---|---|---|---|---|---|---|---|
| Off-Spotter | Yes | Yes | Yes | 0-5 | NGG, NAG, NNNNACA, NNGRRT (R is A or G) | mRNA exons, unspliced mRNA, mRNA, 5'UTR, CDS, 3'UTR, unspliced lincRNA, lincRNA | User customizable | Webserver Source code | [1] |
| CHOPCHOP | No | No | Partial | 0, 2 | NGG, NNAGAA, NNNNGANN | No | Yes | Webserver | [2] |
| CRISPRseek | Yes | Yes | No | Any number | User customizable | mRNA exons | Yes | Source code | [3] |
| sgRNA Designer | No | No | No | 0 | NGG | CDS (if searching by transcript ID) | Yes | Webserver Source code | [4] |
| CRISPR Design | Yes | No | No | 4 | NGG and NAG | mRNA exons | Yes | Webserver | [5] |
| COD | No | No | No | 0, 3, 5, 8 | NGG, NGG and NAG | No | Yes | Webserver | - |
| Cas-OFFinder | Yes | Yes | No | 0-10 | NGG, NRG, NNAGAAW, NNNNGMTT | No | Yes | Webserver Source code | [6] |
References
- ^ Pliatsika V, Rigoutsos I (2015). ""Off-Spotter": very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/ Cas guide RNAs". Biol. Direct. 10 (1): 4. doi:10.1186/s13062-015-0035-z. PMID 25630343.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E (2014). "CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing". Nucleic Acids Res. 42 (W1): W401-7. doi:10.1093/nar/gku410. PMID 24861617.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Zhu LJ, Holmes BR, Aronin N, Brodsky MH (2014). "CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems". PLoS One. 9 (9): e108424. doi:10.1371/journal.pone.0108424. PMID 25247697.
{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link) - ^ Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE (2014). "Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation". Nat Biotechnol. 32 (12): 1262–7. doi:10.1038/nbt.3026. PMID 25184501.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F (2013). "DNA targeting specificity of RNA-guided Cas9 nucleases". Nat Biotechnol. 31 (9): 827–32. doi:10.1038/nbt.2647. PMID 23873081.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Bae S, Park J, Kim JS (2014). "Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases". Bioinformatics. 30 (10): 1473–5. doi:10.1093/bioinformatics/btu048. PMID 24463181.
{{cite journal}}: CS1 maint: multiple names: authors list (link)