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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

Chris22

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Posted 21 April 2017 - 02:07 PM

Hello,

 

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

 

Chris

 

 

 







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