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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...
RNA Splicing01:32

RNA Splicing

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...
RNA Splicing01:32

RNA Splicing

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...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

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Related Experiment Video

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq.

Zheng Xia1, Jianguo Wen, Chung-Che Chang

  • 1Department of Radiology, The Methodist Hospital Research Institute, Houston, TX 77030, USA.

BMC Bioinformatics
|May 18, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new method, Nonnegativity and Sparsity constrained Maximum APosteriori (NSMAP), to identify and quantify novel RNA isoforms from RNA sequencing data without relying on a reference genome. NSMAP improves transcriptome analysis by simultaneously detecting isoform structures and estimating expression levels.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA sequencing (RNA-Seq) is crucial for studying gene expression and alternative splicing.
  • Current RNA-Seq methods often rely on incomplete reference genomes, limiting comprehensive transcriptome analysis.
  • There is a need for methods that can infer and estimate RNA isoforms directly from RNA-Seq data without prior annotation.

Purpose of the Study:

  • To develop a novel computational method for identifying and quantifying RNA isoforms directly from RNA-Seq data.
  • To overcome the limitations of incomplete reference genomes in transcriptome analysis.
  • To enable a more comprehensive investigation of the transcriptome, including novel isoforms.

Main Methods:

  • A Nonnegativity and Sparsity constrained Maximum APosteriori (NSMAP) model was developed.
  • NSMAP simultaneously identifies isoform structures and estimates their expression levels.
  • The model was validated using simulations with real RNA-Seq data.

Main Results:

  • NSMAP correctly identified and quantified over 77% of expressed isoforms in simulations.
  • The method was applied to RNA-Seq data from myelodysplastic syndromes (MDS) samples.
  • NSMAP identified differentially expressed known and novel isoforms in MDS disease.

Conclusions:

  • NSMAP offers a robust strategy for identifying and quantifying novel RNA isoforms.
  • This approach enhances the utility of RNA-Seq for in-depth transcriptome analysis.
  • The NSMAP package is publicly available for research use.