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