SAVoR: a server for sequencing annotation and visualization of RNA structures
Open Access
- 6 April 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 40 (W1), W59-W64
- https://doi.org/10.1093/nar/gks310
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.Keywords
This publication has 29 references indexed in Scilit:
- The Arabidopsis Information Resource (TAIR): improved gene annotation and new toolsNucleic Acids Research, 2011
- NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policyNucleic Acids Research, 2011
- Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA StabilityMolecular Cell, 2011
- High-throughput approaches for plant epigenomic studiesCurrent Opinion in Plant Biology, 2011
- Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavageNucleic Acids Research, 2011
- RNA sequencing: advances, challenges and opportunitiesNature Reviews Genetics, 2010
- FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencingNature Methods, 2010
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiationNature Biotechnology, 2010
- Tfold: efficient in silico prediction of non-coding RNA secondary structuresNucleic Acids Research, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009