CircularLogo: A lightweight web application to visualize intra-motif dependencies

BMC Bioinformatics

Software

Tao Ma¹  Zhenqing Ye²  Surendra Dasari²  Michael T. Kalmbach²  Jean-Pierre A. Kocher²  Liguo Wang³ 

[1] Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA;Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA;Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA;Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA;

关键词: CircularLogo;    Intra-motif dependency;    Visualization;    Interactive;   

DOI  :  10.1186/s12859-017-1680-2

 received in 2016-11-16, accepted in 2017-05-11,  发布年份 2017

来源: Springer

【 摘 要 】

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

【 授权许可】

CC BY   
© The Author(s). 2017