Thus, composition biased regions should be ignored when compiling sequence identity, and be used only to confirm presence of similar composition bias in identified homologues. Evolutionary patterns crucial for successful prediction of function. A typical mistake is to predict function by putative homology based on an over-interpreted level of sequence similarity. Functional and structural constraints are translated into sequence conservation in a particular way that depends on the particular protein structure and its evolution. The level of similarity required for identifying functionally equivalent proteins in two species depends on the overall divergence of the species and on the particular protein family.
Some databases use more reliable annotations than others.
Quality of alignment. Despite the central r le that alignment programs play in sequence analysis, a thorough analysis of the quality of methods based on statistically significant numbers of proteins has yet to be accomplished. Stability of alignment. Not necessarily, the reason may, as well, be that the alignment is just not unique, i.e., the best and the second best solution to the alignment problem may have similar scores. In such cases the alignment is less reliable in regions where the results from A and B differ.