asanmat: An Asymmetric Scaled Ambiguous Nucleotide scoring Matrix...
In cnobles/gintools: Genomic DNA Integration Analysis Tools

View source: R/nucleotide_scoring_matrices.R

Meant for comparing ambiguous sequences against other sequences possibly containing ambiguous nucleotides. The scores are scaled between 0 and 1 for ambiguous matches based on overlaping proportions and the matrix is asymmetric. This is meant for proper scoreing between different ambiguous bases. For example, comparing a "S" (meaning a "C" or "G") to a "V" (meaning a "C", "G", or "A") would be if either nucleotide was chosen (score = 1), but comparing a "V" to an "S" would only be correct 2 out of three times (score = 0.67).Constructed originally from NUC4.4. Function outputs a single square matrix.