Related Experiment Video
Updated: Jun 29, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
Philipp N Seibel1, Tobias Müller, Thomas Dandekar
1Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany. philipp.seibel@biozentrum.uni-wuerzburg.de
Background:
The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. There are several tools available that help performing these tasks, but all of them are specialized and focus on only one aspect, editing the alignment or plotting the secondary structure. The problem is both these tasks need to be performed simultaneously.
Findings:
4SALE is designed to handle sequence and secondary structure information of RNAs synchronously. By including a complete new method of simultaneous visualization and editing RNA sequences and secondary structure information, 4SALE enables to improve and understand RNA sequence and secondary structure evolution much more easily.
Conclusion:
4SALE is a step further for simultaneously handling RNA sequence and secondary structure information. It provides a complete new way of visual monitoring different structural aspects, while editing the alignment. The software is freely available and distributed from its website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de/
Related Concept Videos
RNA Structure
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Nucleic Acid Structure
DNA Structure
DNA has a double-helix structure. The...
RNA Editing

