TY - JOUR T1 - CircularLogo: A lightweight web application to visualize intra-motif dependencies JF - bioRxiv DO - 10.1101/098327 SP - 098327 AU - Zhenqing Ye AU - Tao Ma AU - Michael T. Kalmbach AU - Surendra Dasari AU - Jean-Pierre A. Kocher AU - Liguo Wang Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/02/16/098327.abstract N2 - 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.BEMthe Binding Energy ModelJSONJavaScript Object NotationMEMEMultiple Em for Motif ElicitationMACEModel-based Analysis of ChIP-ExoMIMutual InformationPSSMPosition-Specific Scoring MatrixPMMthe inhomogeneous Parsimonious Markov ModelPWMPosition Weight MatrixTFBSTranscription Factor Binding SitesTFFMsTranscription Factor Flexible Model ER -