What is Similarity Score

The function of proteins is a main subject of research in systems biology. Inference of function is now, more than ever, required by the upcoming of novel protein sequences in consequence of the discovery of new proteomes. The calculation of sequence similarity is an easily feasible way to compute protein comparisons. The comparison of complete proteomes touches one of the earliest topics in bioinformatics; the biologically meaningful organization of proteins in protein families. Several approaches that interpret function or evolutionary aspects of proteins from sequence similarity are reviewed, which in particular reflects the arsenal of techniques introduced until now. Phylogenetic profiling, a method that compares a set of genes or proteins by their presence or absence across a given set of organisms, is also presented in this chapter. Proteins in a functional context, for example, a pathway or a protein complex, are represented by identical or similar phylogenetic profiles. The detection of functional contexts by phylogenetic profiling is also playing a prospective role as an analytic tool in systems biology. Already established tools for phylogenetic profiling as well as particular biological examples based on the SYSTERS protein family data set are presented.