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RNA-seq03:21

RNA-seq

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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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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Genome Annotation and Assembly

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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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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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RNA Structure01:23

RNA Structure

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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.
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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.
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Updated: Nov 10, 2025

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms
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AASRA: an anchor alignment-based small RNA annotation pipeline†.

Chong Tang1,2, Yeming Xie1,2, Mei Guo1

  • 1BGI Genomics, BGI-Shenzhen, Shenzhen, China.

Biology of Reproduction
|March 31, 2021
PubMed
Summary

A new software, AASRA, improves small noncoding RNA sequencing analysis. It accurately annotates all small noncoding RNA types and identifies novel variants, overcoming limitations of existing tools.

Keywords:
RNA-Seqbioinformaticsprecursor microRNAsequence alignmentsmall RNA annotation

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Deep sequencing of small noncoding RNAs (sncRNA-Seq) is standard for detection and quantification.
  • Current sncRNA annotation tools struggle to identify variants and annotate all known sncRNA types simultaneously.

Purpose of the Study:

  • To introduce AASRA, a novel software package for comprehensive sncRNA annotation.
  • To address the limitations of existing tools in variant recognition and simultaneous annotation of diverse sncRNA species.

Main Methods:

  • Development of an anchor alignment-based approach for sncRNA annotation.
  • Implementation of an all-in-one pipeline for high-speed, simultaneous annotation.
  • Capability to differentiate mature microRNAs from precursors and identify novel variants.

Main Results:

  • AASRA enables high-speed, simultaneous annotation of all known sncRNA species.
  • The software successfully distinguishes mature microRNAs from precursor molecules.
  • AASRA identifies novel sncRNA variants within sequencing reads.

Conclusions:

  • AASRA is an efficient and comprehensive tool for sncRNA annotation.
  • This software enhances the analysis of sncRNA-Seq data by improving variant detection and annotation accuracy.
  • AASRA facilitates a deeper understanding of small noncoding RNA populations.