Question: Does CRISPRSEEK work on previously unknown genomes?
gravatar for yhuang2
12 months ago by
yhuang20 wrote:

What genomes are supported by CRISPRSEEK?  Is it possible to analyze novel genomes?  If so, what are the requirements (format of genome file, etc) for the new genome?


ADD COMMENTlink modified 12 months ago by Julie Zhu3.8k • written 12 months ago by yhuang20
gravatar for Julie Zhu
12 months ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:


Thanks for taking time to post the question! lists BSgenomes that can be directly used as input to CRISPRseek .

For detailed information on how to use the package, please read the user guide at and the supplementary file in the following publication

 Zhu LJ, Holmes BR, Aronin N and Brodsky MH (2014). “CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems.” PLoS one, 9(9).

To design guides without available BSgenome, please refer to this post at  CRISPRseek with genome not available in BSgenome. It also talks about analyzing data for novel genome using compare2Sequences function

​Best regards,


ADD COMMENTlink written 12 months ago by Julie Zhu3.8k

Thanks Julie.  This is very helpful. 

ADD REPLYlink written 12 months ago by yhuang20
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