Open BenLangmead opened 5 years ago
It's we could simply draw the PAM sequences in a different color. Since we're already asking users to evaluate the choices visually, this allows them to visually cross-reference the k-mer with the PAM sequence.
This is hard to do for both strands. An NGG sequence is a PAM motif on the forward strand, but it would be CCN on the reverse. Perhaps we could color NGG bases blue and CCN bases red and then bases involved in both (e.g. the middle two bases in CCGG) would be purple?
https://twitter.com/JayPykw/status/1098943811844112384
From CHOPCHOP: "The Cas9/sgRNA complex binds a 20 bp target sequence followed by a 3 bp protospacer adjacent motif (PAM) -NGG (two invariable Gs preceded by a variable base)."