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Related Concept Videos

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...
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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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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

Virtual genetic coding and time series analysis for alternative splicing prediction in C. elegans.

Michele Ceccarelli1, Antonio Maratea

  • 1Research Centre on Software Technologies, University of Sannio, via Traiano 1, 82100 Benevento, Italy. ceccarelli@unisannio.it

Artificial Intelligence in Medicine
|October 22, 2008
PubMed
Summary

This study introduces a novel computational approach for predicting alternative splicing events using only genomic sequences. The method achieves state-of-the-art results by employing virtual genetic coding and time series analysis, enhancing genomic sequence analysis.

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

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • Alternative splicing prediction traditionally relies on expressed sequences, homology, and local sequence features.
  • Recent machine learning approaches aim to reduce reliance on prior information with limited success.

Purpose of the Study:

  • To develop a fully automatic method for alternative splicing event recognition solely from genomic sequences.
  • To establish a numerical modeling approach for sequence information content.
  • To apply time series analysis and machine learning for splicing event prediction.

Main Methods:

  • Introduction of a virtual genetic coding scheme for numerical sequence modeling.
  • Extraction of fixed-length features using time series analysis.
  • Application of a supervised learning method, specifically Support Vector Machine (SVM), for prediction.

Main Results:

  • Demonstrated superior prediction performance compared to state-of-the-art methods using C. elegans data.
  • Achieved high accuracy without explicit modeling of homology or splice site positions.
  • Validated the effectiveness of the purely numerical framework.

Conclusions:

  • Virtual genetic coding combined with time series analysis provides a powerful sequence coding scheme.
  • This approach offers a novel and effective tool for genomics and transcriptomics research.
  • The method advances automated analysis of genomic sequences for splicing events.