TOTEMS: Histogram of Evolutionarily Conserved Amino Acids

We have developed a tool that allows us to easily visualize evolutionary variation via complementary multiple sequence alignments and frequency-based stacked Sequence Logos. This tool, TOTEMS (hisTogram of evOluTionarily consErved aMino acidS), visualizes conserved regions in a multiple sequence alignment within regions of a three-dimensional structure that share similar degrees of evolutionary conservation as revealed in ConSurf output data. Unlike Sequence Logos that illustrate the relative frequency of individual amino acid residues (as in MSAViewer), or moving window averages that focus on properties such as hydrophobicity or electrical charge (as in CATH), TOTEMS can help users discriminate degrees of evolutionary conservation in adjacent positions within a three-dimensional structure. Thus, we offer a tool that serves to complement pre-existing visualization applications such as ConSurf, MSAViewer, and CATH. TOTEMS and its source code are freely available.