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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...
What is Gene Expression?01:36

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...

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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Detecting alternative gene structures from spliced ESTs: a computational approach.

Paola Bonizzoni1, Giancarlo Mauri, Graziano Pesole

  • 1Dipartimento di Informatica Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Milano, Italy. bonizzoni@disco.unimib.it

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|January 6, 2009
PubMed
Summary
This summary is machine-generated.

Alternative splicing (AS) generates proteomic complexity from limited genes. This study introduces computational methods to predict AS events and transcript isoforms from expressed sequence tag data, addressing key algorithmic challenges.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Alternative splicing (AS) is a key mechanism explaining the complexity of the human proteome relative to gene count.
  • Expressed Sequence Tag (EST) data facilitates computational prediction of AS by aligning ESTs to genome sequences.
  • Reconstructing transcript isoforms from ESTs is crucial for understanding AS variations.

Purpose of the Study:

  • Investigate computational challenges in detecting alternative splicing.
  • Analyze algorithmic solutions for predicting alternative splicing and transcript isoforms.
  • Formalize and address the Minimum Exons ESTs Factorization (MEF) problem.

Main Methods:

  • Formalized the Minimum Exons ESTs Factorization (MEF) problem, proving its NP-hard nature.
  • Defined sets of spliced ESTs factorized into constitutive exons.
  • Developed a graph algorithm for predicting transcript isoforms from spliced EST sequences.

Main Results:

  • Demonstrated the NP-hard complexity of predicting splicing sites from ESTs.
  • Proposed a linear-time graph algorithm for transcript isoform prediction.
  • Conducted experimental analysis to evaluate prediction reliability.

Conclusions:

  • Alternative splicing prediction remains a challenging computational problem.
  • The proposed graph algorithm offers an efficient method for isoform prediction.
  • Experimental validation is essential for assessing the reliability of AS prediction methods.