Scripts and protocols to search for cas proteins and CRISPR sequences
Files preparation
ls *.smp > cdd_crispr.pn
makeprofiledb -in cdd_crispr.pn -title cdd_crispr -dbtype 'rps'
perl constructMappingCDD.pl
Cas finding
rpsblast+ -query proteins.faa -db cdd_crispr.pn -evalue 1e-05 -outfmt '6 qseqid sseqid pident qcovs qcovhsp length qlen slen evalue qstart qend sstart send' -max_target_seqs 1 -out output.blast
perl filterRPSBlastOutput.pl output.blast