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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...
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...

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Updated: May 10, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

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

Published on: December 9, 2016

DeepSAP: improved RNA-seq alignment by integrating transcriptome guidance with transformer-based splice junction

Fadel Berakdar1, Thomas D Wu2, Tong Zhu1

  • 1NVIDIA Corporation, 2788 San Tomas Expy, Santa Clara, 95051, CA, USA.

Genome Biology
|May 8, 2026
PubMed
Summary
This summary is machine-generated.

DeepSAP enhances RNA sequencing (RNA-seq) alignment by combining genomic alignment with transformer-based splice-junction scoring. This novel approach significantly improves splice junction detection and the analysis of complex RNA splicing patterns.

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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

Related Experiment Videos

Last Updated: May 10, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

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:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput sequencing has transformed transcriptomics, but RNA-seq analysis faces challenges with complex splice junctions and multi-mapped reads.
  • Accurate splice junction detection is crucial for understanding gene expression, splicing variations, and chimeric events.

Purpose of the Study:

  • To introduce DeepSAP, a novel computational tool designed to improve RNA-seq alignment accuracy.
  • To enhance the detection of splice junctions, indels, and complex splicing patterns in RNA-seq data.

Main Methods:

  • DeepSAP integrates GSNAP's transcriptome-guided genomic alignment with transformer-based splice-junction scoring.
  • The method leverages deep learning to analyze sequence patterns around splice donor and acceptor sites.

Main Results:

  • DeepSAP achieved the highest mean F1-score for splice junction detection on the Baruzzo human simulated benchmark.
  • It outperformed established tools including DRAGEN, novoSplice, STAR, HISAT2, and Subjunc across various complexity levels.
  • The tool demonstrated superior performance in identifying indels and resolving complex splicing events.

Conclusions:

  • DeepSAP represents a significant advancement in RNA-seq alignment and analysis.
  • Its ability to capture intricate sequence patterns improves the accuracy of splice junction detection and the resolution of complex splicing, advancing transcriptomic research.