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Get PAMs

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nyoungb2 edited this page Sep 19, 2013 · 2 revisions

WARNING: spacer blasts must be done prior!

Get PAMs (from spacer BLASTs) for 1 CRISPR subtype (I-B)

$ CLdb_getPAMs.pl -da CLdb.sqlite -subtype I-B > I-B_pam.fasta

Make a weblogo of the alignment

$ weblogo < I-B_pam.fasta -F pdf -c "classic" --errorbars NO > I-B_pam_weblogo.pdf