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Genomics

Installing CRISPRCasFinder on Ubuntu

Dr. Muniba Faiza

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install crisprcasfinder on ubuntu

CRISPR/Cas9 is a genome editing technology trending fastly. It is used to identify CRISPR associated genes within the genomes of prokaryotic bacterias. Several tools are available for this. Amongst them, CRISPRCasFinder is one that is used to search for CRISPRs and Cas genes in sequence data [1]. In this article, we will install CRISPRCasFinder on Ubuntu.

Preparing

Update and upgrade your system. Open a terminal and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading CRISPRCasFinder

Download the zip file using the following command:

$ wget https://crisprcas.i2bc.paris-saclay.fr/Home/DownloadFile?filename=CRISPRCasFinder.zip

Installing CRISPRCasFinder

Now, unzip the file and change to the directory

$ unzip CRISPRCasFinder.zip

$ cd CRISPRCasFinder/

$ bash installer_UBUNTU.sh

$ source ~/.profile

Running CRISPRCasFinder

After successful installation, it can be easily run using the Perl script as shown below:

$ perl CRISPRCasFinder.pl -in <input file> -cas -cf CasFinder-2.0.3 -def G -keep


Reference

  1. Couvin, D., Bernheim, A., Toffano-Nioche, C., Touchon, M., Michalik, J., Néron, B., … & Pourcel, C. (2018). CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic acids research46(W1), W246-W251.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

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How to install Cortex on Ubuntu?

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Installing BCFtools on Ubuntu

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