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Related Concept Videos

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...
Pre-mRNA Processing: RNA Splicing01:32

Pre-mRNA Processing: 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-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...
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...
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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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

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.

Yanju Zhang1, Eric-Wubbo Lameijer, Peter A C 't Hoen

  • 1Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands. y.zhang@lumc.nl

Bioinformatics (Oxford, England)
|January 6, 2012
PubMed
Summary

We developed PASSion, a novel pipeline for detecting splice sites in RNA sequencing (RNA-Seq) data. PASSion accurately identifies known and novel splicing events, outperforming existing tools, especially for abundant transcripts.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA sequencing (RNA-Seq) is crucial for transcriptome profiling and understanding disease etiology linked to splicing abnormalities.
  • Accurate mapping of RNA-Seq reads spanning exon-exon boundaries to the reference genome presents a significant challenge.
  • Identifying splice junctions is key to cellular phenotyping and disease research.

Purpose of the Study:

  • To develop a robust pipeline for splice site detection in paired-end RNA-Seq reads.
  • To evaluate the performance of the developed pipeline against existing RNA-Seq analysis tools.
  • To enable the discovery of novel and differential splicing patterns.

Main Methods:

  • Development of PASSion, a pattern growth algorithm-based pipeline for splice site detection.
  • Comparative analysis of PASSion against TopHat, MapSplice, and HMMSplicer using public RNA-Seq datasets.
  • Assessment of pipeline performance irrespective of read length and coverage.

Main Results:

  • PASSion demonstrates competitive performance compared to established pipelines.
  • PASSion's accuracy is unaffected by read length and sequencing coverage.
  • The pipeline excels at detecting junctions in highly abundant transcripts and identifies novel splicing motifs.
  • PASSion predicted a substantial number of splicing events, including a significant percentage of novel junctions.
  • The tool can identify differential and shared splicing patterns across multiple samples.

Conclusions:

  • PASSion offers a powerful and versatile tool for splice site detection in RNA-Seq data.
  • The pipeline enhances the ability to discover novel splicing events and analyze complex splicing patterns.
  • PASSion provides a valuable resource for transcriptomic studies, particularly in disease research involving splicing alterations.