BayesFold allows you to display additional data about a structure by color-coding the nucleotide text and/or the pair connectors using the coloring option in the Format palette (see Section 3, “Understanding the Format Palette”). Based on the color mode , these data can either be expressed in color or greyscale. The possible coloring options are detailed below.
Base text colorings:
base: each base is colored by which nucleotide it is (A, G, C, or U.)
pairs: each base in an alleged pair is colored by the pair type (A with U, C with G, and U with G). Mismatched pairs are colored red.
mismatch: each base in an alleged pair is colored by whether it represents a strict mismatch (comprised of two bases that can never pair), a loose mismatch (comprised of two degenerate bases that can sometimes pair), or a strict match (comprised of two bases that must always pair.)
percent occupied: each base is colored by the fraction of sequences that have a base at its position in the sequence alignment.
information: each base is colored by the Shannon uncertainty at its position in the sequence alignment, subtracted from two.
motifs: each base is colored by the user-defined motif that it is part of (if any). See Section 4, “Working with Motifs” for additional information on motifs.
Pair connector colorings:
pair probability: each pair connector is colored by the average probability of that pair across all sequences.
mutual information: each pair connector is colored by the mutual information score for its constituent nucleotides' positions in the sequence alignment.
fraction pairable: each pair connector is colored by the fraction of sequences in which that pair is actually valid.
For additional information on scale and more details about the calculations of percent occupied, information, pair probability, mutual information, and fraction pairable, see Section 4, “Understanding the Kinds of Evidence”.