Figure 3

Example of profile logos from LogoMat and Skylign. Particular focus is placed on gap parameter visualization, using a section of the Pfam Pkinase protein domain (Pfam accession PF00069). Positions 137 and 148 both have high probability of being followed by an insertion (29% and 53%, respectively), with modest expected insert length (7.7 and 4.5, respectively). Position 148 also has a low occupancy (70%). (A) The logo produced by LogoMat, which represents gap parameters by stretching in the horizontal plane. Positions with low occupancy are given less horizontal space, but this is difficult to see. Insert rate and expected length are represented with variable-width red and pink columns. (B) Skylign simplifies visual interpretation of gap parameters by presenting a three row table beneath the letter stacks. The top row shows occupancy, with stronger blue background indicating lower occupancy. The middle row presents insert probability, and the bottom row shows expected insert length. For both insert rows, a stronger red background indicates higher values. Note that the default expected insert length (1.9) depends on the priors used when constructing the HMM; observed shorter or longer inserts can shift the expected length away from this value. When a cell in the middle row (insert probability) is not white, a thin red vertical bar of matching color is drawn immediately after the position for that cell, indicating that the insertion will produce letters between the neighboring positions.