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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...
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...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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

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Supersplat--spliced RNA-seq alignment.

Douglas W Bryant1, Rongkun Shen, Henry D Priest

  • 1Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.

Bioinformatics (Oxford, England)
|April 23, 2010
PubMed
Summary
This summary is machine-generated.

Supersplat is a new method for discovering splice junctions using RNA-sequencing data. This tool enables unbiased identification of intron/exon boundaries, aiding in genome annotation.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • High-throughput sequencing enables detailed analysis of expressed transcript sequences.
  • Identifying intron/exon boundaries is crucial for accurate genome annotation but remains challenging.

Purpose of the Study:

  • To present supersplat, a novel method for unbiased splice-junction discovery.
  • To provide an efficient tool for empirical RNA-sequencing data analysis.

Main Methods:

  • Supersplat utilizes empirical RNA-sequencing data for splice-junction discovery.
  • The method is implemented in C++ and operates on genomic references.

Main Results:

  • Supersplat identifies potential splice junctions at a rate of ~11.4 million reads per hour.
  • The algorithm was benchmarked using Illumina RNA-seq reads on Arabidopsis thaliana.
  • Its utility for de novo splice junction annotation was demonstrated on Brachypodium distachyon.

Conclusions:

  • Supersplat offers an efficient and unbiased approach for splice-junction discovery.
  • The tool facilitates improved genome annotation through empirical RNA-seq data analysis.