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Literature DB >> 25089276

SSFinder: high throughput CRISPR-Cas target sites prediction tool.

Santosh Kumar Upadhyay¹, Shailesh Sharma¹.

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets. The SSFinder is a user-friendly tool, compatible with Windows, Mac OS, and Linux operating systems, and freely available online.

Entities: Disease Gene Species

Mesh：

Year: 2014 PMID： 25089276 PMCID： PMC4095993 DOI： 10.1155/2014/742482

Source DB: PubMed Journal: Biomed Res Int Impact factor: 3.411

13 in total

Review 1. TALENs: customizable molecular DNA scissors for genome engineering of plants.

Authors: Kunling Chen; Caixia Gao
Journal: J Genet Genomics Date: 2013-03-26 Impact factor: 4.275

2. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria.

Authors: Giedrius Gasiunas; Rodolphe Barrangou; Philippe Horvath; Virginijus Siksnys
Journal: Proc Natl Acad Sci U S A Date: 2012-09-04 Impact factor: 11.205

3. Structural basis for CRISPR RNA-guided DNA recognition by Cascade.

Authors: Matthijs M Jore; Magnus Lundgren; Esther van Duijn; Jelle B Bultema; Edze R Westra; Sakharam P Waghmare; Blake Wiedenheft; Umit Pul; Reinhild Wurm; Rolf Wagner; Marieke R Beijer; Arjan Barendregt; Kaihong Zhou; Ambrosius P L Snijders; Mark J Dickman; Jennifer A Doudna; Egbert J Boekema; Albert J R Heck; John van der Oost; Stan J J Brouns
Journal: Nat Struct Mol Biol Date: 2011-04-03 Impact factor: 15.369

4. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

Authors: Lei S Qi; Matthew H Larson; Luke A Gilbert; Jennifer A Doudna; Jonathan S Weissman; Adam P Arkin; Wendell A Lim
Journal: Cell Date: 2013-02-28 Impact factor: 41.582

5. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9.

Authors: Jian-Feng Li; Julie E Norville; John Aach; Matthew McCormack; Dandan Zhang; Jenifer Bush; George M Church; Jen Sheen
Journal: Nat Biotechnol Date: 2013-08 Impact factor: 54.908

6. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells.

Authors: Yanfang Fu; Jennifer A Foden; Cyd Khayter; Morgan L Maeder; Deepak Reyon; J Keith Joung; Jeffry D Sander
Journal: Nat Biotechnol Date: 2013-06-23 Impact factor: 54.908

7. RNA-guided genome editing for target gene mutations in wheat.

Authors: Santosh Kumar Upadhyay; Jitesh Kumar; Anshu Alok; Rakesh Tuli
Journal: G3 (Bethesda) Date: 2013-12-09 Impact factor: 3.154

8. RNA-programmed genome editing in human cells.

Authors: Martin Jinek; Alexandra East; Aaron Cheng; Steven Lin; Enbo Ma; Jennifer Doudna
Journal: Elife Date: 2013-01-29 Impact factor: 8.140

9. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system.

Authors: David Bikard; Wenyan Jiang; Poulami Samai; Ann Hochschild; Feng Zhang; Luciano A Marraffini
Journal: Nucleic Acids Res Date: 2013-06-12 Impact factor: 16.971

10. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets.

Authors: Ambarish Biswas; Joshua N Gagnon; Stan J J Brouns; Peter C Fineran; Chris M Brown
Journal: RNA Biol Date: 2013-03-14 Impact factor: 4.652

16 in total

1. CRISPR/Cas9-mediated efficient editing in phytoene desaturase (PDS) demonstrates precise manipulation in banana cv. Rasthali genome.

Authors: Navneet Kaur; Anshu Alok; Navjot Kaur; Pankaj Pandey; Praveen Awasthi; Siddharth Tiwari
Journal: Funct Integr Genomics Date: 2017-11-29 Impact factor: 3.410

2. An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants.

Authors: Ajay Prakash Uniyal; Komal Mansotra; Sudesh Kumar Yadav; Vinay Kumar
Journal: 3 Biotech Date: 2019-05-21 Impact factor: 2.406

3. CRISPR/Cas9-Mediated CCR5 Ablation in Human Hematopoietic Stem/Progenitor Cells Confers HIV-1 Resistance In Vivo.

Authors: Lei Xu; Huan Yang; Yang Gao; Zeyu Chen; Liangfu Xie; Yulin Liu; Ying Liu; Xiaobao Wang; Hanwei Li; Weifeng Lai; Yuan He; Anzhi Yao; Liying Ma; Yiming Shao; Bin Zhang; Chengyan Wang; Hu Chen; Hongkui Deng
Journal: Mol Ther Date: 2017-05-17 Impact factor: 11.454

Review 4. Understanding the DNA damage response in order to achieve desired gene editing outcomes in mosquitoes.

Authors: Justin M Overcash; Azadeh Aryan; Kevin M Myles; Zach N Adelman
Journal: Chromosome Res Date: 2015-02 Impact factor: 5.239

Review 5. Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools.

Authors: Alessandro Laganà; Dennis Shasha; Carlo Maria Croce
Journal: Front Bioeng Biotechnol Date: 2014-12-11

6. ge-CRISPR - An integrated pipeline for the prediction and analysis of sgRNAs genome editing efficiency for CRISPR/Cas system.

Authors: Karambir Kaur; Amit Kumar Gupta; Akanksha Rajput; Manoj Kumar
Journal: Sci Rep Date: 2016-09-01 Impact factor: 4.379