SAVoR: a server for sequencing annotation and visualization of RNA structures

Abstract

RNA secondary structure is required for the proper regulation of the cellular transcriptome. This is because the functionality, processing, localization and stability of RNAs are all dependent on the folding of these molecules into intricate structures through specific base pairing interactions encoded in their primary nucleotide sequences. Thus, as the number of RNA sequencing (RNA-seq) data sets and the variety of protocols for this technology grow rapidly, it is becoming increasingly pertinent to develop tools that can analyze and visualize this sequence data in the context of RNA secondary structure. Here, we present Sequencing Annotation and Visualization of RNA structures (SAVoR), a web server, which seamlessly links RNA structure predictions with sequencing data and genomic annotations to produce highly informative and annotated models of RNA secondary structure. SAVoR accepts read alignment data from RNA-seq experiments and computes a series of per-base values such as read abundance and sequence variant frequency. These values can then be visualized on a customizable secondary structure model. SAVoR is freely available at http://tesla.pcbi.upenn.edu/savor.

Figure 1.

The SAVoR workflow. Upon validation of user input, the primary sequence and genomic location of the user-submitted transcript(s) are determined, and intersecting sequence reads are converted to the desired annotation values. The secondary structure is then determined and plotted with the specified visualization options.

Figure 2.

SAVoR can be used to visualize RNA-seq results in the context of predicted RNA secondary structures. In this example, the ‘User Input’ tab of the SAVoR web interface is populated with a sample input. The desired transcript is specified by UCSC-style genomic coordinates, and a custom structure is provided in dot-parenthesis notation. The ‘coverage’ annotation type has been selected and the URL for a web-accessible BAM file of read alignments provided. All optional visualization settings have been selected, and a blue-red color scheme will be used.

Figure 3.

SAVoR produces highly informative, user specified, annotated models of RNA secondary structure. The ‘Output’ tab of the SAVoR web interface is dynamically rendered to show progress indicators and error messages. Each step of the pipeline is indicated, and a ‘Complete’ message appears upon successful completion. When the entire process is finished, the output (an annotated model of RNA secondary structure) is displayed, and links for downloading the output files are provided. Additionally, the calculated per-base annotation values are displayed in tabular form and can be downloaded as a plain text file.