Phylo-mLogo

An interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

Arthur Chun Chieh Shih, D. T. Lee, Chin Lin Peng, Yu Wei Wu

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Background: When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences 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 alignments of many sequences. Results: A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. 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 of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. 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. Conclusion: With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL http://biocomp.iis.sinica.edu.tw/phylomlogo.

Original languageEnglish
Article number63
JournalBMC Bioinformatics
Volume8
DOIs
Publication statusPublished - 2007
Externally publishedYes

Fingerprint

Sequence Alignment
Alignment
Visualization
Position-Specific Scoring Matrices
Viruses
Entropy
Phylogeny
Sequence Homology
Orthomyxoviridae
Virus
History
Amino Acids
Influenza
Amino acids
Websites
Genes
Homogeneity
Gene
Calculate

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

Phylo-mLogo : An interactive and hierarchical multiple-logo visualization tool for alignment of many sequences. / Shih, Arthur Chun Chieh; Lee, D. T.; Peng, Chin Lin; Wu, Yu Wei.

In: BMC Bioinformatics, Vol. 8, 63, 2007.

Research output: Contribution to journalArticle

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