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Related Concept Videos

RNA-seq03:21

RNA-seq

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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...
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RNA Stability01:53

RNA Stability

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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RNA Splicing01:32

RNA Splicing

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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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Related Experiment Video

Updated: Jan 28, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

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Holistic optimization of an RNA-seq workflow for multi-threaded environments.

Ling-Hong Hung1, Wes Lloyd1, Radhika Agumbe Sridhar1

  • 1School of Engineering and Technology, Tacoma, WA, USA.

Bioinformatics (Oxford, England)
|March 13, 2019
PubMed
Summary
This summary is machine-generated.

Optimizing all steps in a unique molecular identifier RNA-sequencing pipeline, not just alignment, significantly boosts speed. Full pipeline optimization with 16 threads shows an 8-fold improvement over single-threaded and 4-fold over parallel implementations.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-generation sequencing (NGS) pipelines involve computationally intensive steps, primarily read alignment.
  • Alignment software like Burrows-Wheeler Aligner is optimized for speed and cloud parallelization.
  • Other pipeline steps can also be optimized for significant speed increases, especially with multi-threading.

Purpose of the Study:

  • To evaluate the impact of optimizing non-alignment steps in a unique molecular identifier (UMI) RNA-sequencing pipeline.
  • To compare the speed improvements from optimizing the entire pipeline versus only the alignment step.

Main Methods:

  • Development and implementation of an optimized UMI RNA-sequencing pipeline with three steps: split, align, and merge.
  • Performance benchmarking of the optimized pipeline against the original implementation using single and multiple threads (16 threads).

Main Results:

  • Optimizing all three pipeline steps (split, align, merge) resulted in a 40% speed increase with a single thread.
  • Using 16 threads, the fully optimized pipeline showed a 4-fold improvement over the original parallel version and an 8-fold improvement over the original single-threaded version.
  • Optimizing only the alignment step yielded a modest 13% improvement over the original parallel workflow with 16 threads.

Conclusions:

  • Comprehensive optimization of all steps in an UMI RNA-sequencing pipeline is crucial for maximizing computational efficiency.
  • Focusing solely on optimizing the alignment step provides limited gains compared to a holistic optimization approach.
  • The developed optimized pipeline offers substantial speedups for UMI RNA-sequencing data processing.