CircularLogo: A light weighted web application to visualize intra-motif dependencies

Abstract BackgroundThe 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. ResultWe 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. ConclusionCircularLogo is an innovative web application that specifically designed to visualize and explore intra-motif dependencies.