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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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
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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Updated: May 13, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

Modelling splice sites with locality-sensitive sequence features.

Sing-Wu Liou1, Yin-Fu Huang

  • 1Graduate School of Engineering Science and Technology, National Yunlin University of Science and Technology, 123 University Road, Section 3, Touliu, Yunlin, Taiwan 640, ROC. g9110808@yuntech.edu.tw

International Journal of Data Mining and Bioinformatics
|February 27, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces Locality Sensitive Features (LSFs) to improve Splice Site Modelling (SSM) by bridging gaps in sequence analysis. The new LSF-based method shows robust and versatile performance across diverse species for splice-site classification.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

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Last Updated: May 13, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

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

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Splice sites are critical for pre-mRNA maturation and Splice Site Modelling (SSM).
  • Existing computational methods face challenges in accurately identifying sequence features corresponding to splicing signals.
  • Gaps persist between biological splicing signals and computationally derived sequence features.

Purpose of the Study:

  • To propose Locality Sensitive Features (LSFs) to bridge the gap between splicing signals and computational sequence features.
  • To enhance Splice Site Modelling (SSM) by homogenizing feature contexts using LSFs.
  • To develop a robust and versatile methodology for splice-site classification.

Main Methods:

  • Introduction of Locality Sensitive Features (LSFs) for context homogenization.
  • Application of skewness-kurtosis based statistics and data analysis.
  • Implementation of double-boundary outlier filters for SSM.
  • Validation across six diverse model organisms.

Main Results:

  • LSF-based SSM demonstrated promising accuracy and robustness.
  • Receiver Operating Characteristic (ROC) analysis confirmed the methodology's effectiveness.
  • The approach proved versatile across different species.

Conclusions:

  • LSF-based SSM offers a novel infrastructure for splice-site prediction.
  • The methodology shows potential for application in other sequence prediction problems.
  • This approach enhances the accuracy and reliability of splice-site classification.