Estimating residue evolutionary conservation by introducing von Neumann entropy and a novel gap-treating approach

Abstract

Evolutionary conservation derived from a multiple sequence alignment is a powerful indicator of the functional significance of a residue, and it can help to predict active sites, ligand-binding sites, and protein interaction interfaces. The results of the existing algorithms in identifying the residue's conservation strongly depend on the sequence alignment, making the results highly variable. Here, by introducing the amino acid similarity matrix, we propose a novel gap-treating approach by combining the evolutionary information and von Neumann entropies to compute the residue conservation scores. It is indicated through a series of tested results that the new approach is quite encouraging and promising and may become a useful tool in complementing the existing methods.

Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment

“…Deduced amino acid sequences from our obtained sequences were aligned using MUSCLE (Edgar, 2004) together with the corresponding region of the reference protein sequences. Gap-treated Shannon entropy (H′) (Zhang et al , 2007) at each alignment position was calculated as: $${H^{\prime }}_i=-\sum _{a=1}^{20}{f}_{i,a}{log}_{20}{f}_{i,a}+f_{i,\mathrm{italicgap}}$$ where f i,a is the relative frequency of amino acid a at the alignment position i. f i,gap represents the number of gaps at the alignment position i divided by the number of alignment sequences.…”

Novel Biphenyl-Oxidizing Bacteria and Dioxygenase Genes from a Korean Tidal Mudflat

“…The phylogenetic tree of ARHD amino acid sequences was constructed after alignment by MUSCLE (7) with MEGA4 (13). In order to compare the conserved region with the well-known dioxygenases from Pfam, an amino acid conservation analysis was carried out using ARHD sequences (9,23). The experimental details are described in the supplemental material.…”

Conservation in mitochondrial DNA: Parallelized estimation and alignment influence

“…Furthermore, we have deeply studied the impact of the alignment in identifying the conservation of residues (nucleotides or amino acids). The alignment method selected along with its parameters can make the results highly variable [10]. Our results proving this statement are based on the analysis of different sets of aligned sequences-the differences between these sets are not only based on the type of residue, but also on the taxonomic classification of each of them, i.e.…”