Date of this Version
Nucleic Acids Research
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.
© The Author(s) 2012. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
base pairing, base sequence, genome, secondary protein structure, RNA sequence analysis, RNA, molecule, datasets
Li, F., Ryvkin, P., Childress, D. M., Valladares, O., Gregory, B. D., & Wang, L. (2012). SAVoR: A Server for Sequencing Annotation and Visualization of RNA Structures. Nucleic Acids Research, 40 (W1), W59-W64. http://dx.doi.org/10.1093/nar/gks310
Date Posted: 14 July 2017
This document has been peer reviewed.