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Related Concept Videos

RNA Structure01:19

RNA Structure

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...
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...
RNA Structure01:23

RNA Structure

Overview
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Different Types of RNA Have the Same Basic Structure
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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. 
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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
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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Analyzing and Building Nucleic Acid Structures with 3DNA
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SARSA: a web tool for structural alignment of RNA using a structural alphabet.

Yen-Fu Chang1, Yen-Lin Huang, Chin Lung Lu

  • 1Institute of Bioinformatics, National Chioa Tung University, Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan.

Nucleic Acids Research
|May 27, 2008
PubMed
Summary

SARSA is a web tool that aligns RNA tertiary structures by converting them into sequences. This approach enables efficient comparison and identification of structural similarities and motifs.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • RNA tertiary structures are complex and require specialized tools for comparison.
  • Existing methods may not efficiently capture subtle structural similarities.

Purpose of the Study:

  • To introduce SARSA, a novel web tool for aligning RNA tertiary structures.
  • To provide tools for both pairwise (PARTS) and multiple (MARTS) RNA structure alignment.

Main Methods:

  • Utilizes vector quantization to derive a structural alphabet (SA) of 23 nucleotide conformations.
  • Transforms 3D RNA structures into 1D SA-encoded sequences.
  • Employs classical sequence alignment algorithms for structural comparison.

Main Results:

  • SARSA offers four pairwise alignment types: global, semi-global, local, and normalized local.
  • PARTS and MARTS can align RNA 3D structures from PDB files.
  • Outputs include graphical displays for visual inspection of superimposed aligned structures.

Conclusions:

  • SARSA provides an effective method for comparing RNA tertiary structures.
  • The tool facilitates the detection of structural motifs and similarities through sequence-based alignment of structural alphabets.