The comparison of protein and DNA sequences is an important analytical method of applied bioinformatics. The annotations of new nucleotide and protein sequences, construction of model structures for proteins, design and analysis of expression studies, and a variety of other bioinformatic and biological experiments are all based on these analyses. Nature acts conservatively, i.e., it does not develop a new kind of biology for every life form but continuously changes and adapts a proven general concept. Novel functionalities do not appear because a new gene has suddenly arisen but are developed and modified during evolution. Given this situation, therefore, one may transfer functional information from one protein to another if both possess a certain degree of similarity. However, this process must be carried out critically because similar proteins may yet perform different functions. The similarity of two proteins can arise based on evolution from a common ancestor (convergent evolution) or independently of each other based on different ancestor proteins (divergent evolution).