Exploring comprehensive within-motif dependence of transcription factor binding in Escherichia coli

DepLogo: visualizing sequence dependencies in R

SUMMARY

Statistical dependencies are present in a variety of sequence data, but are not discernible from traditional sequence logos. Here, we present the R package DepLogo for visualizing inter-position dependencies in aligned sequence data as dependency logos. Dependency logos make dependency structures, which correspond to regular co-occurrences of symbols at dependent positions, visually perceptible. To this end, sequences are partitioned based on their symbols at highly dependent positions as measured by mutual information, and each partition obtains its own visual representation. We illustrate the utility of the DepLogo package in several use cases generating dependency logos from DNA, RNA and protein sequences.

AVAILABILITY AND IMPLEMENTATION

The DepLogo R package is available from CRAN and its source code is available at https://github.com/Jstacs/DepLogo.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

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

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.