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標題: Phylo-mLogo: An interactive multiple-logo visualization tool for large-number sequence alignments
作者: Shih, Arthur Chun-Chieh
Peng, Chin-Lin
Wu, Yu-Wei
關鍵字: alignment visualization, sequence logo, influenza, avian influenza
Project: BMC Bioinformatics, Volume�8, Issue 63.
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.
Appears in Collections:資訊科學與工程學系所

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