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Related Concept Videos

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...
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...
Leaky Scanning02:28

Leaky Scanning

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 stands for...
CRISPR and crRNAs02:53

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
RNA Structure01:23

RNA Structure

Overview
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...

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Updated: May 9, 2026

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Chain-RNA: a comparative ncRNA search tool based on the two-dimensional chain algorithm.

Jikai Lei1, Prapaporn Techa-Angkoon, Yanni Sun

  • 1Michigan State University, East Lansing, MI 48824, USA.

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|August 10, 2013
PubMed
Summary
This summary is machine-generated.

Identifying noncoding RNAs (ncRNAs) is crucial. Chain-RNA, a new tool, excels at finding evolutionarily conserved ncRNAs by analyzing both sequence and structure, outperforming traditional methods.

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Last Updated: May 9, 2026

Identification of Circular RNAs using RNA Sequencing
08:25

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Published on: November 14, 2019

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11:01

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Published on: April 30, 2026

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07:35

Computational Analysis Tutorial for Chimeric Small Noncoding RNA: Target RNA Sequencing Libraries

Published on: December 1, 2023

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Noncoding RNA (ncRNA) identification is vital for modern biology.
  • Comparative genomics, using sequence and secondary structure conservation, is the standard for ncRNA detection.
  • Traditional local alignment tools like BLAST have low sensitivity for ncRNAs with low sequence conservation but high structural similarity.

Purpose of the Study:

  • To develop a novel method for identifying cross-species conserved RNA elements with low sequence similarity.
  • To introduce chain-RNA, a pairwise structural alignment tool that integrates both sequence and structural information for ncRNA detection.

Main Methods:

  • Chain-RNA extracts stem-loop structures from dot plots generated by a local-folding algorithm.
  • Stem alignment is framed as an extended 2D chain problem, utilizing existing chain algorithms.
  • The tool was tested on annotated ncRNA homologs and applied to novel ncRNA discovery in transcriptomic data.

Main Results:

  • Chain-RNA demonstrates a superior trade-off between sensitivity and false positive rate compared to conventional sequence similarity search tools.
  • The tool exhibits greater time efficiency than existing structural alignment tools.
  • Successful application in identifying novel ncRNAs within transcriptomic datasets.

Conclusions:

  • Chain-RNA offers an effective approach for identifying ncRNAs, particularly those with limited sequence conservation.
  • The method enhances ncRNA discovery by combining sequence and structural analysis.
  • Chain-RNA provides a valuable, efficient, and sensitive tool for genomic and transcriptomic research.