Here you will the scripts and data associated with the research article "Search for PAM sequences associated with CRISPR-Cas systems in Pseudomonas aeruginosa and their enrichment in plasmids and phages" [under preparation]. A brief comment on the purpose of each script is provided here:
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script1_spacers_df.R Construction of the Pseudomonas aeruginosa spacers dataframe for the
df2fasta()function of the Spacer2PAM library. The spacers were collected from the output of CRISPRCasFinder and filtered based on known CRISPR-Cas array orientation and evidence level equal to 4, and known subtype determined by CRISPRCas-Typer. -
script2_PAM_prediction.R After the information regarding each spacer has been collected, the PAM for each CRISPR-Cas subtype will be predicted using Spacer2PAM.
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script3_PLSDB_IMGVR_sequences_filtering.sh From the PLSDB database v2020_06_23_v2 and the IMG/VR v3 high-quality genomes database, the Pseudomonas aeruginosa sequences will be filtered.
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script4_plasmids_viruses_BLAST.sh The spacers representing each Pseudomonas aeruginosa CRISPR-Cas subtype will be blasted against the P. aeruginosa plasmids and viruses from the PLSDB and IMG/VR databases, respectively (an example is provided for P. aeruginosa CRISPR-Cas subtype I-C and IMG/VR database).
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script5_DNA_logos_plasmids_viruses.R For the P. aeruginosa plasmids and viruses from the PLSDB and IMG/VR databases, respectively, that are recognized by each Pseudomonas aeruginosa CRISPR-Cas system subtype, the DNA logo will be constructed (an example is provided for P. aeruginosa CRISPR-Cas subtype I-C and IMG/VR database).
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script6_PAM_freq_GC.sh Determination of the occurrence of the PAM and GC content in the foreign sequences (plasmids and viruses from the PLSDB and IMG/VR databases, respectively) recognized by each Pseudomonas aeruginosa CRISPR-Cas system (an example is provided for P. aeruginosa CRISPR-Cas subtype I-C and IMG/VR database).