Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Parallel Processing01:20

Parallel Processing

888
The brain processes sensory information rapidly due to parallel processing, which involves sending data across multiple neural pathways at the same time. This method allows the brain to manage various sensory qualities, such as shapes, colors, movements, and locations, all concurrently. For instance, when observing a forest landscape, the brain simultaneously processes the movement of leaves, the shapes of trees, the depth between them, and the various shades of green. This enables a quick and...
888
Improving Translational Accuracy02:07

Improving Translational Accuracy

15.5K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
15.5K
Improving Translational Accuracy02:07

Improving Translational Accuracy

3.8K
3.8K
RNA-seq03:21

RNA-seq

12.5K
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...
12.5K
Sanger Sequencing01:57

Sanger Sequencing

778.5K
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...
778.5K
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

7.6K
Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
7.6K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A decade of progress towards the elimination of hepatitis C: from the National Strategic Plan to Artificial Intelligence.

Gastroenterologia y hepatologia·2026
Same author

Menopause age and hypercholesterolemia comorbidities: a region-wide retrospective cohort study in Andalusia, Spain (2016-2022).

BMJ open·2026
Same author

IMPaCT-Data: A Federated Precision Medicine Infrastructure Associated with Science and Technology in Spain.

Studies in health technology and informatics·2026
Same author

National dialysis registry of the Dominican Republic: first nationwide epidemiological analysis of renal replacement therapy.

BMC nephrology·2026
Same author

High-Fidelity Synthetic Data Replicates Clinical Prediction Performance in a Million-Patient Diabetes Cohort.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

Cocirculation of endemic and recently introduced West Nile Virus lineage 1 clades in Southern Spain.

One health (Amsterdam, Netherlands)·2026
Same journal

circ2DGNN: circRNA-Disease Association Prediction via Transformer-Based Graph Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Hierarchical Hypergraph Learning in Association- Weighted Heterogeneous Network for miRNA- Disease Association Identification.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Discriminative Domain Adaption Network for Simultaneously Removing Batch Effects and Annotating Cell Types in Single-Cell RNA-Seq.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

MLW-BFECF: A Multi-Weighted Dynamic Cascade Forest Based on Bilinear Feature Extraction for Predicting the Stage of Kidney Renal Clear Cell Carcinoma on Multi-Modal Gene Data.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

An End-to-End Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Generative Biomedical Event Extraction With Constrained Decoding Strategy.

IEEE/ACM transactions on computational biology and bioinformatics·2024
See all related articles

Related Experiment Video

Updated: Apr 1, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.8K

Concurrent and Accurate Short Read Mapping on Multicore Processors.

Héctor Martínez, Joaquín Tárraga, Ignacio Medina

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |October 10, 2015
    PubMed
    Summary
    This summary is machine-generated.

    HPG Aligner SA is a new parallel RNA sequence aligner that rapidly maps RNA fragments using suffix arrays and Smith-Waterman for accuracy. It outperforms existing tools in speed and sensitivity for analyzing RNA reads.

    More Related Videos

    Mapping Mammalian 3D Genome Interactions with Micro-C-XL
    11:41

    Mapping Mammalian 3D Genome Interactions with Micro-C-XL

    Published on: November 3, 2023

    4.0K
    Transcription Start Site Mapping Using Super-low Input Carrier-CAGE
    06:59

    Transcription Start Site Mapping Using Super-low Input Carrier-CAGE

    Published on: June 26, 2019

    12.7K

    Related Experiment Videos

    Last Updated: Apr 1, 2026

    Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
    14:06

    Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

    Published on: June 23, 2012

    15.8K
    Mapping Mammalian 3D Genome Interactions with Micro-C-XL
    11:41

    Mapping Mammalian 3D Genome Interactions with Micro-C-XL

    Published on: November 3, 2023

    4.0K
    Transcription Start Site Mapping Using Super-low Input Carrier-CAGE
    06:59

    Transcription Start Site Mapping Using Super-low Input Carrier-CAGE

    Published on: June 26, 2019

    12.7K

    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Genomics

    Background:

    • Accurate mapping of RNA sequences is crucial for understanding gene expression and regulation.
    • Existing RNA sequence aligners face challenges with speed and accuracy, especially for large datasets.
    • Multicore processors offer significant computational power for complex bioinformatics tasks.

    Purpose of the Study:

    • To develop a fast and accurate parallel RNA sequence aligner for multicore processors.
    • To improve the efficiency and sensitivity of RNA sequence mapping.
    • To provide an open-source solution for the research community.

    Main Methods:

    • Developed HPG Aligner SA, a parallel aligner utilizing a workflow organization.
    • Employed suffix arrays for rapid mapping of RNA fragments (reads).
    • Integrated the Smith-Waterman algorithm for accurate alignment of conflictive reads.
    • Implemented an adaptive strategy for splice junction detection using RNA read segmentation (seeds).

    Main Results:

    • HPG Aligner SA demonstrates superior parallel performance on Intel multicore platforms.
    • The aligner excels in execution time and sensitivity compared to state-of-the-art tools like TopHat 2+Bowtie 2, MapSplice, and STAR.
    • Successfully mapped a large fraction of RNA fragments with high accuracy.
    • Effective detection of splice junctions was achieved through the seeding strategy.

    Conclusions:

    • HPG Aligner SA offers a significant advancement in RNA sequence alignment speed and accuracy.
    • The software provides a powerful and efficient tool for analyzing RNA sequencing data on modern multicore architectures.
    • HPG Aligner SA is a valuable open-source resource for the bioinformatics and genomics research community.