# Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties

## Fig 2

Comparison of GISMO to five other MSA programs.

As described in the text, for each analysis the CDD test sets were first ordered based on the property specified on the x-axis and then split into four equal-sized partitions. The x-coordinates for all data points are averages, for the property in question, over the test sets assigned to the various partitions; similarly, the GISMO ΔSP-scores for each program are averages taken over these partitions. **A**. GISMO ΔSP-scores as a function of the number of sequences. For comparison, an additional, leftmost set of data points (shown with back-glow) corresponds to 162 out of 218 Balibase 3 test sets; for the remaining 56 Balibase sets, GISMO failed to find a statistically significant alignment presumably due to sparse data: some of these sets have as few as 4 sequences. **B**.GISMO ΔSP-scores as a function of the number of truncated sequences, as defined in the text. **C**. GISMO ΔSP-scores as a function of the ratio between the domain length and mean sequence length. For sequence sets with low ratios, the shared domain is more challenging to align due to a larger search space. **D**. GISMO ΔSP-scores as a function of average relative entropy (with respect to a standard background amino acid distribution and expressed in nats, with 1 nat = 1/ln(2) bits) over all column positions in each benchmark MSA; sequence diversity can be understood as inversely related to relative entropy. For sequence sets with low relative entropy, the shared domain is more difficult to align due to weaker conservation.