The analysis of the characteristics of two or more proteins can result in comparison of their mutual or totally different characteristics and as a result can lead in obtaining general conclusion about determining their function. Although comparative methods give substantial results, we would like to point out that including the so called, “logical” determination will mean that functional predictions can be greatly improved by focusing on how the genes became similar in sequence (i.e., evolution) rather than on the sequence similarity itself . This evolutionary perspective method, based on phylogenetic analysis, will separate only the relevant data, thus simplifying the function prediction and making it more accurate. From the obtained results we can conclude that the combination of phylogenetic analysis with comparative methods results in better accuracy in prediction.
Protein function prediction, Phylogenetic analysis, Gene Ontology, C4.5 Classification