This repository gives access to the code used to perform data analysis on CRISPR arrays deep-sequenced using Illumina MiSeq.
All sequence alignments were performed using command-line BLAST. An example of a command used to perform an alignment between a CRISPR locus sequence and the repeat sequence is shown below:
blastn -query locus_sequence.fasta -subject Repeat.fasta -task blastn-short -ungapped -num_threads 32 -outfmt 6 -out locus_sequence.blastnSimilar BLAST commands were used to perform the alignments between the newly acquired spacers and the reference sequences.
The Python file acquisition.py counts of the number of new spacers acquired and then extracts them and sends them to a FASTA file containing all new spacers. The file spacer_align.py helps find the origin of each newly acquired spacer.
PAM_extraction.py was then used to extract PAMs and see if they matched the expected motif.