Amino acid conservation.zip

We analyzed the degree of conservation at each position in the multiple sequence alignment (MSA), taking into account of biochemical similarity between amino acids.
In our experiments, we compared conservation index (CI) to other state-of-art conservation methods (i.e. Shannon entropy, Jensen-Shannon diversity score [2], Relative Entropy [2], von Neumann entropy [2]). We found that CI was a robust estimation of the conserved sites for three merits: (1) positions with no natural variations in the MSA have equal CIs using our method. This is not the case in Jensen-Shannon diversity score, for instance. (2) The more the natural variations are observed in a position, the higher the CIs. This is not the case for relative entropy and von Neumann entropy, for instance. (3) The biochemical similarity between amino acids is taken into account. This is not the case in Shannon entropy where all amino acids are treated equally.
Citation: Guangdi Li, Jens Verheyen, Soo-Yon Rhee, Arnout Voet, Anne-Mieke Vandamme, Kristof Theys. Functional conservation of HIV-1 gag: implications for rational drug design. Retrovirology 2013, 10:126 (Impact factor=5.6)