CasOT specifications

Information


Unique identifier OMICS_04701
Name CasOT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Genome sequence files, a genome annotation file, an input file including individual 21–33-nt target sites.
Input format FASTA, GTF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 1.0
Stability No
Maintained No

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Publication for CasOT

CasOT in publications

 (18)
PMCID: 5851096
PMID: 29534717
DOI: 10.1186/s12934-018-0887-x

[…] (soe) pcr. the resulting homologous arm was then inserted into the bamhi/hindiii-digested pseva-gricf, thus creating pseva-grict., here, the n20 sequence of low off-target rate was designed via casot []. n20 sequences of all pseva-grnat derivatives were constructed by two reverse primers with 20 nt reverse complementarity. the repairing homologous arms were ligated into pseva-grnat by bamhi […]

PMCID: 5787926
PMID: 29378572
DOI: 10.1186/s12934-018-0867-1

[…] the target dna sequence. we used the pila promoter from m. xanthus to drive the transcription of sgrna. the off-target efficiency of spacer was calculated by using the 1.0 version of the software casot []. because a spacer with high off-target efficiency does not function well in the transcriptional activation [–], four spacers (epoact2, 3, 4 and 5) were designed having low off-target […]

PMCID: 5865846
PMID: 28944845
DOI: 10.3892/mmr.2017.7518

[…] by the crispr/cas9 system was evaluated. finally, the combined inhibition of crispr/cas9 system and etv was assessed., sgrnas were designed using the crispr/cas system (cas9/grna) off-targeter (casot) tool (http://casot.cbi.pku.edu.cn/; peking university, beijing, china) to minimize potential off-target effects. the sequences of six sgrnas targeting dhbv genome (genbank: k01834.1) and one […]

PMCID: 5428692
PMID: 28360425
DOI: 10.1038/s41598-017-00501-4

[…] we designed a 20-bp grna and a17–18 bp tru-grna for the target mutagenesis of sliaa9. target sequences were selected in silico using the grna design website “focas”. in this website, the casot algorithm is used to find potential off-target sites, suggesting an off-target score, and an “on_target_score_calculator.py” algorithm is used to evaluate on-target activity. using these tools, […]

PMCID: 5355646
PMID: 28238795
DOI: 10.1016/j.stemcr.2017.01.022

[…] post-excision clones were pcr amplified and sequenced. amplicons were analyzed by sanger sequencing., to predict potential ot effects, guide sequences sgrna-a and sgrna-b () were analyzed using the casot script () and the top-ranked hits were selected for screening. selected genomic regions were amplified and amplicons were then mixed in a 1:1 ratio of parental (cag180):corrected (hd-c#1, #2 […]


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CasOT institution(s)
Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Center for Bioinformatics, College of Life Sciences, Peking University, Beijing, China; State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences, Peking University, Beijing, China; Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
CasOT funding source(s)
Supported by National Natural Science Foundation of China (NSFC) [31110103904], the 973 programs [2011CBA01000, 2012CB945101, 2011CBA01102], and NSFC [31171242].

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