Related Experiment Video
Updated: Apr 27, 2026
06:59
Nanomanipulation of Single RNA Molecules by Optical Tweezers
Published on: August 20, 2014
14.5K
A new approach for detecting riboswitches in DNA sequences
Jessen T Havill1, Chinmoy Bhatiya1, Steven M Johnson1
1Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
Bioinformatics (Oxford, England)
|July 13, 2014
Summary
The Denison Riboswitch Detector (DRD) tool rapidly identifies potential riboswitches in bacterial genomes. This computational method offers high accuracy, aiding researchers in understanding gene expression regulation.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Riboswitches are RNA sequences that regulate gene expression by altering their structure.
- Computational prediction of riboswitches aids molecular biologists in studying gene regulation.
Purpose of the Study:
- To introduce the Denison Riboswitch Detector (DRD), a novel computational tool for identifying riboswitches.
- To provide a user-friendly web interface for rapid riboswitch detection in large DNA sequences.
Main Methods:
- Developed a computational algorithm that models riboswitch detection as a 'heaviest path' problem on a multipartite graph.
- Utilized efficient dynamic programming to solve the graph problem.
- Implemented the algorithm in a web-accessible tool, DRD.
Main Results:
- The Denison Riboswitch Detector (DRD) can identify putative riboswitches in DNA sequences at the scale of bacterial genomes.
- DRD demonstrates high performance with approximately 88-99% sensitivity and over 99.99% specificity across 13 riboswitch families.
- The tool allows for easy modification and creation of riboswitch descriptions.
Conclusions:
- DRD is an effective and accurate computational tool for identifying riboswitches.
- The tool facilitates research into riboswitch-mediated gene expression regulation.
- DRD is accessible via a web interface for broad scientific use.
Related Concept Videos
01:56Riboswitches
8.0K
Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
8.0K
01:23Transcriptional Regulation: Riboswitches
1.2K
Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
1.2K
01:23Types of RNA
61.2K
Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
61.2K
02:24Ribosome Profiling
3.2K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.2K
01:29Translational Regulation
869
Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
869
03:21RNA-seq
9.2K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.2K