| 词条 | CRISPR/Cas Tools | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 释义 |
CRISPR/Cas Tools are software platforms and bioinformatics tools built to facilitate the design of guide RNAs (gRNAs) for use with the CRISPR/Cas system. CRISPR/CasThe CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR associated nucleases) system was originally discovered to be an acquired immune response mechanism used by archaea and bacteria. It has since been adopted for use as a tool in the genetic engineering of higher organisms. Designing an appropriate gRNA is an important element of genome editing with the CRISPR/Cas system. A gRNA can and at times does have unintended interactions ("off-targets") with other locations of the genome of interest. For a given candidate gRNA, these tools report its list of potential off-targets in the genome thereby allowing the designer to evaluate its suitability prior to embarking on any experiments. Scientists have also begun exploring the mechanics of the CRISPR/Cas system and what governs how good, or active, a gRNA is at directing the Cas nuclease to a specific location of the genome of interest.[1][1] As a result of this work, new methods of assessing a gRNA for its 'activity' have been published,[1][1] and it is now best practice to consider both the unintended interactions of a gRNA as well as the predicted activity of a gRNA at the design stage. TableThe below table lists available tools and their attributes, and includes links to the corresponding websites.
References1. ^1 {{Cite journal|title = Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach|journal = Nature Methods|date = 2015-01-01|doi = 10.1038/nmeth.3473|first = Raj|last = Chari|first2 = Prashant|last2 = Mali|first3 = Mark|last3 = Moosburner|first4 = George M|last4 = Church|volume=12|issue = 9|pages=823–826|pmid=26167643|pmc = 5292764}} {{DEFAULTSORT:CRISPR Cas Tools}}2. ^{{Cite journal|last=Oliveros|first=Juan C.|last2=Franch|first2=Mònica|last3=Tabas-Madrid|first3=Daniel|last4=San-León|first4=David|last5=Montoliu|first5=Lluis|last6=Cubas|first6=Pilar|last7=Pazos|first7=Florencio|date=2016-07-08|title=Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes|journal=Nucleic Acids Research|volume=44|issue=W1|pages=W267–271|doi=10.1093/nar/gkw407|issn=1362-4962|pmc=4987939|pmid=27166368}} 3. ^{{cite journal |vauthors=Bae S, Park J, Kim JS | title = Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases | journal = Bioinformatics | volume = 30 | issue = 10 | pages = 1473–5 | year = 2014 | pmid = 24463181 | doi = 10.1093/bioinformatics/btu048 | pmc=4016707}} 4. ^{{Cite journal|last=Enkler|first=Ludovic|last2=Richer|first2=Delphine|last3=Marchand|first3=Anthony L.|last4=Ferrandon|first4=Dominique|last5=Jossinet|first5=Fabrice|date=2016-10-21|title=Genome engineering in the yeast pathogen Candida glabrata using the CRISPR-Cas9 system|journal=Scientific Reports|volume=6|pages=35766|doi=10.1038/srep35766|issn=2045-2322|pmc=5073330|pmid=27767081|bibcode=2016NatSR...635766E}} 5. ^{{cite journal |vauthors=Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL | title = CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool | journal = PLOS ONE | volume = 10 | issue = 4 | pages = e0124633 | year = 2015 | pmid = 25909470 | doi = 10.1371/journal.pone.0124633 | pmc=4409221| bibcode = 2015PLoSO..1024633S }} 6. ^{{cite journal |vauthors=Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E | title = CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing | journal = Nucleic Acids Res. | volume = 42 | issue = W1 | pages = W401–7 | year = 2014 | pmid = 24861617 | doi = 10.1093/nar/gku410 | pmc=4086086}} 7. ^{{cite journal |vauthors = Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E | title = CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering | journal = Nucleic Acids Res. | volume = 44 | issue = W1 | pages = W272–6 | year = 2016 | pmid = 27185894 | doi = 10.1093/nar/gkw398 | pmc=4987937}} 8. ^{{cite journal |vauthors=Haeussler, Schoenig, Eckert et al. | title = Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR | journal = Genome Biology | volume = 17 | issue = 1 | pages = 148 | year = 2016 | pmid = 27380939 | doi=10.1186/s13059-016-1012-2 | pmc=4934014}} 9. ^{{cite journal |vauthors=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 | title = DNA targeting specificity of RNA-guided Cas9 nucleases | journal = Nat. Biotechnol. | volume = 31 | issue = 9 | pages = 827–32 | year = 2013 | pmid = 23873081 | doi = 10.1038/nbt.2647 | pmc=3969858| hdl = 1721.1/102691 }} 10. ^{{cite journal |vauthors=Naito Y, Hino K, Bono H, Ui-Tei K | title = CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites | journal = Bioinformatics | volume = 31 | issue = 7 | pages = 1120–3 | year = 2015 | pmid = 25414360 | doi = 10.1093/bioinformatics/btu743 | pmc=4382898}} 11. ^{{cite journal |vauthors=Zhu LJ, Holmes BR, Aronin N, Brodsky MH | title = CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems | journal = PLOS ONE | volume = 9 | issue = 9 | pages = e108424 | year = 2014 | pmid = 25247697 | doi = 10.1371/journal.pone.0108424 | pmc=4172692| bibcode = 2014PLoSO...9j8424Z }} 12. ^{{ cite news | title = Desktop Genetics Announces the Launch of DeskGen Gene Editing Platform | journal = American Laboratory | year = 2015 | url = http://www.americanlaboratory.com/173625-Desktop-Genetics-Announces-the-Launch-of-DeskGen-Gene-Editing-Platform/ }} 13. ^1 2 3 {{cite journal |vauthors=Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE | title = Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation | journal = Nat. Biotechnol. | volume = 32 | issue = 12 | pages = 1262–7 | year = 2014 | pmid = 25184501 | doi = 10.1038/nbt.3026 | pmc=4262738}} 14. ^{{Cite journal|last=O’Brien|first=Aidan|last2=Bailey|first2=Timothy L.|date=2014-09-15|title=GT-Scan: identifying unique genomic targets|url=https://academic.oup.com/bioinformatics/article/30/18/2673/2475622/GT-Scan-identifying-unique-genomic-targets|journal=Bioinformatics|volume=30|issue=18|pages=2673–2675|doi=10.1093/bioinformatics/btu354|issn=1367-4803|pmc=4155256|pmid=24860161}} 15. ^{{cite journal |vauthors=Pliatsika V, Rigoutsos I | title = "Off-Spotter": very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/ Cas guide RNAs | journal = Biol. Direct | volume = 10 | issue = 1 | pages = 4 | year = 2015 | pmid = 25630343 | doi = 10.1186/s13062-015-0035-z | pmc=4326336}} 16. ^TechCrunch. [https://techcrunch.com/2017/05/16/synthegos-genetic-toolkit-aims-to-make-crispr-more-accessible/ "Synthego’s genetic toolkit aims to make CRISPR more accessible | May 2017"] Retrieved 23 January 2018. 1 : Genetic engineering |
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