CircularLogo

A lightweight web application to visualize intra-motif dependencies

Zhenqing Ye, Tao Ma, Michael T. Kalmbach, Surendra Dasari, Jean-Pierre Kocher, Liguo Wang

Research output: Contribution to journalArticle

Abstract

Background: The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available for visualization. Result: We developed CircularLogo, a web-based interactive application, which is able to not only visualize the position-specific nucleotide consensus and diversity but also display the intra-motif dependencies. Applying CircularLogo to HNF6 binding sites and tRNA sequences demonstrated its ability to show intra-motif dependencies and intuitively reveal biomolecular structure. CircularLogo is implemented in JavaScript and Python based on the Django web framework. The program's source code and user's manual are freely available at http://circularlogo.sourceforge.net. CircularLogo web server can be accessed from http://bioinformaticstools.mayo.edu/circularlogo/index.html. Conclusion:CircularLogo is an innovative web application that is specifically designed to visualize and interactively explore intra-motif dependencies.

Original languageEnglish (US)
Article number269
JournalBMC Bioinformatics
Volume18
Issue number1
DOIs
StatePublished - May 22 2017

Fingerprint

Nucleotide Motifs
Nucleotides
Position-Specific Scoring Matrices
Web Application
Binding sites
Transfer RNA
RNA
Boidae
DNA
Servers
Visualization
Binding Sites
JavaScript
Python
Web Server
Web-based
Quantify

Keywords

  • CircularLogo
  • Interactive
  • Intra-motif dependency
  • Visualization

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

CircularLogo : A lightweight web application to visualize intra-motif dependencies. / Ye, Zhenqing; Ma, Tao; Kalmbach, Michael T.; Dasari, Surendra; Kocher, Jean-Pierre; Wang, Liguo.

In: BMC Bioinformatics, Vol. 18, No. 1, 269, 22.05.2017.

Research output: Contribution to journalArticle

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