Does the quality of the input alignment matter?
While CFG Analysis seems to be fairly resilient to minor errors in the sequence alignment, a manually-curated alignment may well enchance the chances of accurately predicting the location of a functional site. Any information that could lead to an improved alignment – such as secondary structure or other structural information – should therefore be given due consideration when preparing the input data. As tends to be the case with sequence/structure-based functional prediction methodologies, exerting good judgment during the preparation of the input will generally enhance the likelihood of success.
