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Related Concept Videos

lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA (lncRNA)...
RNA-seq03:21

RNA-seq

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 microarray-based...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...

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Related Experiment Video

Updated: May 20, 2026

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Searching for non-coding RNAs in genomic sequences using ncRNAscout.

Michael Bao1, Miguel Cervantes Cervantes, Ling Zhong

  • 1Bioinformatics Center, New Jersey Institute of Technology, Newark, NJ 07102, USA.

Genomics, Proteomics & Bioinformatics
|July 10, 2012
PubMed
Summary

Discovering novel non-coding RNA (ncRNA) is challenging. The ncRNAscout tool uses sequence and structure to accurately identify and locate these important regulatory molecules within genomes.

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RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
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RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

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Novel Sequence Discovery by Subtractive Genomics
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Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Related Experiment Videos

Last Updated: May 20, 2026

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
09:36

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

Published on: April 10, 2018

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Non-coding RNA (ncRNA) molecules play crucial roles in gene expression regulation.
  • Identifying novel ncRNAs is difficult due to the absence of start/stop codons.
  • Existing methods rely on sequence motifs or structural parameters.

Purpose of the Study:

  • To develop an ab initio tool for discovering novel ncRNA sequences.
  • To integrate both sequence and structural features for enhanced ncRNA detection.

Main Methods:

  • Developed ncRNAscout, an ab initio ncRNA finder.
  • Incorporated sequence frequency, structural stability (t-score), and pattern frequency measures.
  • Utilized known ncRNAs and genomic data for training and validation.

Main Results:

  • ncRNAscout accurately identifies and locates significant numbers of ncRNA sequences.
  • The method effectively combines sequence and structural information for detection.
  • Demonstrated high performance in finding novel ncRNAs within a given genome.

Conclusions:

  • ncRNAscout offers an effective approach for novel non-coding RNA discovery.
  • The tool enhances the identification of functional ncRNA genes.
  • Available for download, facilitating further ncRNA research.