I know that with a reduced DNA/RNA alphabet, both N and - are used to calculate the weight of a given position.
Since the web interface doesn't have a setting to explicitly set extended DNA as an alphabet type, I was wondering how WebLogo handles ambiguous codes (either amino acid or nucleotide)?
Is it like MEME or TAMO in that ambiguous letters or "ignored" (outside of N, X, *, and - --> which seem to be used exclusively for weight calculations)?
I know that with a reduced DNA/RNA alphabet, both
Nand-are used to calculate the weight of a given position.Since the web interface doesn't have a setting to explicitly set
extended DNAas an alphabet type, I was wondering how WebLogo handles ambiguous codes (either amino acid or nucleotide)?Is it like MEME or TAMO in that ambiguous letters or "ignored" (outside of
N,X,*, and---> which seem to be used exclusively for weight calculations)?