Ambiguous nucleotides

[irenekaregi]

Hi,
How does cd-hit-est handle ambiguous nucleotide characters (R, Y, K, N) during clustering? If they are ignored in the word filter, what is a good way to work around this?

Thank you

[ycfywy]

You can set ’R, Y, K' as 'N'. like this:

seq = seq.replace("U", "T")
seq = re.sub(r"[^ACGTN]", "N", seq)