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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...
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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ARH: predicting splice variants from genome-wide data with modified entropy.

Axel Rasche1, Ralf Herwig

  • 1Department of Vertebrate Genomics, Max-Planck-Institute for Molecular Genetics, Ihnestr. 63-73, D-14195 Berlin, Germany. rasche@molgen.mpg.de

Bioinformatics (Oxford, England)
|November 6, 2009
PubMed
Summary

We developed a new method for predicting alternative splicing (AS) events using exon arrays. This entropy-based approach, called ARH, accurately predicts splice variants and overcomes biases in existing methods.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Exon arrays enable genome-wide quantitative study of alternative splicing (AS).
  • Existing AS prediction methods for exon arrays often rely on correlation or ANOVA.
  • A novel information theoretic approach based on entropy is introduced.

Purpose of the Study:

  • To develop a robust prediction method for alternative splicing (AS) using exon array data.
  • To address inherent biases in AS analysis, such as dependency on exon number or expression levels.
  • To evaluate the performance of the new method against existing approaches.

Main Methods:

  • Developed an alternative splicing robust prediction method based on entropy (ARH).
  • Implemented ARH using an information theoretic concept modifying the entropy function.
  • Compared ARH performance with eight existing splicing prediction methods using benchmark data.

Main Results:

  • The ARH method demonstrates robustness against biases in AS analysis.
  • ARH effectively handles dependencies on exon number and variable exon expression.
  • ARH outperforms existing methods in predicting splice variants based on experimental data.

Conclusions:

  • ARH is a well-performing new method for alternative splicing prediction.
  • The entropy-based approach offers an improvement over existing methods for exon array analysis.
  • ARH provides a valuable tool for quantitative AS studies on a genome-wide scale.