RT Journal Article
SR Electronic
T1 CircularLogo: A light weighted web application to visualize intra-motif dependencies
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 098327
DO 10.1101/098327
A1 Zhenqing Ye
A1 Tao Ma
A1 Michael T. Kalmbach
A1 Jean-Pierre A. Kocher
A1 Liguo Wang
YR 2017
UL http://biorxiv.org/content/early/2017/01/04/098327.abstract
AB Background The sequence logo has been widely used to represent DNA or RNA motif for more than three decades. Despite its intelligibility and intuitiveness, the sequence logo is unable to display and reveal the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs.Result We developed CircularLogo, a web-based interactive application that is able to not only visualize the position-specific nucleotide consensus and diversity but also unveil the intra-motif dependencies. When applying it to HNF6 binding sites and tRNA sequences, we demonstrated CircularLogo could display intra-motif dependencies and reveal biomolecular structure effectively. CircularLogo is implemented in Javascript and Python based on the Django web framework. Source code and a comprehensive user’s manual are freely available at http://circularlogo.sourceforge.net. The web server can be accessed from http://bioinformaticstools.mayo.edu/circularlogo/index.html.Conclusion CircularLogo is an innovative web application that specifically designed to visualize and 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