get protospacers

This is a workflow for getting protospacers from a spacer blast table

• See spacer blast if you have not yet performed the spacer BLAST

• Your blast table must be in the output format: '7 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen btop'

• blastdbcmd will be used to pull out the protospacers from the blast database of interest. The comment lines in the blast table will specify the blast database.

• The full length protospacers and protospacers + 5'/3' extensions (default of 10bp) will be appended as new columns to the blast table.

$ CLdb_spacerBlastGetProto.pl < spacer_groups_filtered_blast.txt > spacer_groups_filt_proto_blast.txt

• for more information on the output:

$ perldoc CLdb_spacerBlastGetProto.pl

write out a fasta of the protospacers

$ CLdb_spacerBlastGetProto.pl < spacer_groups_filt_proto_blast.txt > spacer_groups_filt_proto_blast.fasta