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Pipeline to search bacterial CRISPR spacers against specific phage genomes?

CRISPR Bioinformatics Spacers CRISPR tools

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#1 Chris22



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Posted 21 April 2017 - 02:07 PM



This question relates to CRISPR as a bacterial defense mechanism and not the commercial CRISPR uses.


I have a collection of CRISPR spacer arrays from specific bacterial genomes.

I also have a collection of corresponding phage genomes.


I would like to know if someone is aware of a bioinformatic pipeline tool (similar to CRISPRdetect/CRISPRfinder/etc) that can take a collection of spacers and screen against one phage genome, or a collection of phage genomes.


Currently I am BLASTing or using Clustal alignments, but with 100 to 500 different spacers and many genomes, this becomes an issue.


Is there a tool available that can do this efficiently if both spacers and genomes are provided?


Thank you in advance






#2 christinaroberts



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Posted 25 March 2021 - 02:11 AM

Researchers have found an unprecedented defense mechanism by which bacteria defend themselves against invading viruses. When the bacterial immune system gets overwhelmed, the CRISPR-Cas system produces a chemical signal that activates a second enzyme which helps in degrading the invaders' genetic material. There are multiple biotechnology consulting firms that have experts in solving the CRISPR problem allowing people to live a longer and healthier life. This process is very similar to an antiviral mechanism of the human innate immune system.

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