ArticleBMC bioinformatics2007
Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 28 citations in OpenAlex.
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- An evolutionary link between capsular biogenesis and surface motility in bacteria.Nature reviews. Microbiology · 2015Review
- Turning Escherichia coli into a Frataxin-Dependent Organism.PLoS genetics · 2015Article
- ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.BMC proceedings · 2014Article
- BlockLogo: visualization of peptide and sequence motif conservation.Journal of immunological methods · 2013Article
- Exploring the molecular epidemiology and evolutionary dynamics of influenza A virus in Taiwan.PloS one · 2013Article
- Intercity spread of echovirus 6 in Shandong Province, China: application of environmental surveillance in tracing circulating enteroviruses.Applied and environmental microbiology · 2012Article
- A novel metal transporter mediating manganese export (MntX) regulates the Mn to Fe intracellular ratio and Neisseria meningitidis virulence.PLoS pathogens · 2011Article
- Monoamine neurotransmitters as substrates for novel tick sulfotransferases, homology modeling, molecular docking, and enzyme kinetics.ACS chemical biology · 2011Article
- Article
- Phylodynamics and molecular evolution of influenza A virus nucleoprotein genes in Taiwan between 1979 and 2009.PloS one · 2011Article
- Sequence determinants of innate immune activation by short interfering RNAs.BMC immunology · 2009Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhen 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.
resultsA 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.
conclusionWith 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.
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