title: SSFinder: high throughput CRISPR-Cas target sites prediction tool.
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.
authors.affiliation: National Agri-Food Biotechnology Institute, Department of Biotechnology, Government of India, C-127, Industrial Area, S.A.S. Nagar, Phase 8, Mohali, Punjab 160071, India.
authors.forename: Santosh Kumar
authors.identifier: 0000-0001-6991-0502
authors.initials: SK
authors.lastname: Upadhyay
authors.affiliation: National Agri-Food Biotechnology Institute, Department of Biotechnology, Government of India, C-127, Industrial Area, S.A.S. Nagar, Phase 8, Mohali, Punjab 160071, India.
authors.forename: Shailesh
authors.initials: S
authors.lastname: Sharma
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D064113:CRISPR-Cas Systems / Q000235:genetics*; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics*; D018390:Gene Targeting / Q000379:methods*; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D011381:Programming Languages; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
references.citation: J Genet Genomics. 2013 Jun 20;40(6):271-9
references.pmid: 23790626
references.citation: G3 (Bethesda). 2013 Dec 09;3(12):2233-8
references.pmid: 24122057
references.citation: RNA Biol. 2013 May;10(5):817-27
references.pmid: 23492433
references.citation: Nat Struct Mol Biol. 2011 May;18(5):529-36
references.pmid: 21460843
references.citation: Cell. 2013 Feb 28;152(5):1173-83
references.pmid: 23452860
references.citation: Nat Biotechnol. 2013 Sep;31(9):822-6
references.pmid: 23792628
references.citation: Science. 2013 Feb 15;339(6121):823-6
references.pmid: 23287722
references.citation: Nat Biotechnol. 2013 Aug;31(8):688-91
references.pmid: 23929339
references.citation: Science. 2013 Feb 15;339(6121):819-23
references.pmid: 23287718
references.citation: Elife. 2013 Jan 29;2:e00471
references.pmid: 23386978
references.citation: Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):12028-33
references.pmid: 20508152
references.citation: Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):E2579-86
references.pmid: 22949671
references.citation: Nucleic Acids Res. 2013 Aug;41(15):7429-37
references.pmid: 23761437