Phylo-mLogo: An interactive multiple-logo visualization tool for large-number sequence alignments

Abstract

When aligning several hundreds or thousands of sequences, such as HIVs, dengue virus, and influenza viruses, to reconstruct the epidemiological history or to understand the mechanisms of epidemic virus evolution, how to analyze and visualize the large-number alignment results has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the large-number alignments. In this paper, we present a multiple-logo alignment visualization tool, called Phylo-mLogo, which allows the user to visualize the global profile of whole multiple sequence alignment and to hierarchically visualize homologous logos of each clade simultaneously. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment but also demonstrates their local logos for each clade. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the sites of their amino acid changes when analyzing large-number human or avian influenza virus sequences.