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Related Concept Videos

RNA-seq03:21

RNA-seq

9.4K
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...
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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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...
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RNA Structure01:23

RNA Structure

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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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RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. 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) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
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RNA Structure01:23

RNA Structure

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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Updated: May 2, 2026

The ITS2 Database
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The ITS2 Database

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Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems.

Lei Shang, David P Gardner, Weijia Xu

    BMC Systems Biology
    |February 26, 2014
    PubMed
    Summary
    This summary is machine-generated.

    Accurate RNA sequence alignment is crucial for understanding cellular functions and microbial ecology. New CRWAlign programs offer superior speed and accuracy for analyzing extensive RNA sequencing data, especially bacterial 16S rRNA sequences.

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    The ITS2 Database
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    RNA Secondary Structure Prediction Using High-throughput SHAPE
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    A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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    A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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    Area of Science:

    • Molecular Biology
    • Bioinformatics
    • Microbial Ecology

    Background:

    • RNA analysis has expanded beyond its traditional focus on structure and function.
    • RNA's role in cellular processes is increasingly recognized.
    • Ribosomal RNA (rRNA) sequencing is vital for microbial ecology studies.

    Purpose of the Study:

    • To develop and evaluate new computational tools for accurate and rapid RNA sequence alignment.
    • To improve the analysis of large-scale RNA sequencing data.

    Main Methods:

    • Two programs, CRWAlign-1 and CRWAlign-2, were developed using the RNA Comparative Analysis Database (rCAD).
    • These programs utilize phylogenetic, secondary structure, and sequence information to create profiles for alignment.
    • New sequences are aligned to existing template alignments from the Comparative RNA Web (CRW) Site.

    Main Results:

    • CRWAlign programs demonstrated superior accuracy and speed compared to eight other alignment methods.
    • Performance was evaluated on 16S rRNA alignments with varying sequence identities (50-100%).

    Conclusions:

    • CRWAlign programs are suitable for aligning the vast amounts of RNA sequencing data generated by next-generation sequencing.
    • These tools address the growing need for rapid and accurate alignment of bacterial 16S rRNA sequences for microbiome identification.