Details
Critical Description
A user preference and interactive setting to change whether gaps are counted in the Physicochemical property calculation.
Current defaults are hardcoded: conservation is only reported for columns containing 25% or less gaps, and the gap character is treated like any other amino acid symbol (i.e. it has 'all properties') if it is more than 3% abundant.
Ideally, one should be able:
1. Ignore gapped sites in the property calculation.
2. Ignore %age gaps when deciding whether to report conservation, or adjust that threshold.
Current defaults are hardcoded: conservation is only reported for columns containing 25% or less gaps, and the gap character is treated like any other amino acid symbol (i.e. it has 'all properties') if it is more than 3% abundant.
Ideally, one should be able:
1. Ignore gapped sites in the property calculation.
2. Ignore %age gaps when deciding whether to report conservation, or adjust that threshold.