The advantage is that users need not become experts for sequence analysis tools. However, the ease of offering and accessing predictions bears two problems. Users may misinterpret results due to a lack of insight into the features of prediction methods. Higher values for sequence similarity. A rule of thumb for true homologues is that for these similarity scores are higher than identity scores.
Similarity scores depend on the particular similarity metric used.
Thus, results cannot be compared directly between different methods. There are two possible errors in inferring homology from a given level of pairwise sequence identity. 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.