Related Experiment Video
Updated: Mar 31, 2026
08:23
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
4.3K
Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences
Sumit Mukherjee1, Supratim Sengupta1
1Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India.
Bioinformatics (Oxford, England)
|November 1, 2015
Summary
Riboswitches are RNA molecules that regulate gene expression. Riboswitch Scanner is a new tool for rapid and accurate detection of these important genetic elements in genomic sequences.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Riboswitches are regulatory non-coding RNA found in 5' untranslated regions.
- They bind specific metabolites to control gene expression.
- Accurate identification is crucial for understanding their cellular roles.
Purpose of the Study:
- To introduce Riboswitch Scanner, a novel web application.
- To provide an automated pipeline for riboswitch detection.
Main Methods:
- Utilizes a profile Hidden Markov Model (pHMM)-based approach.
- Designed for rapid detection in genomic sequences.
- Achieves high sensitivity and specificity.
Main Results:
- Riboswitch Scanner enables automated riboswitch identification.
- The tool processes both partial and complete genomic sequences.
- Demonstrates high speed, sensitivity, and specificity.
Conclusions:
- Riboswitch Scanner facilitates efficient discovery of riboswitches.
- This aids in elucidating their regulatory functions.
- The application is freely accessible online.
Related Concept Videos
01:56Riboswitches
10.1K
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...
10.1K
01:23Transcriptional Regulation: Riboswitches
1.1K
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...
1.1K
02:24Ribosome Profiling
4.3K
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...
4.3K
01:23Types of RNA
73.9K
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...
73.9K
02:28Leaky Scanning
5.9K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.9K
01:29Translational Regulation
810
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,...
810