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

Sanger Sequencing01:57

Sanger Sequencing

771.8K
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...
771.8K
DNA Microarrays02:34

DNA Microarrays

20.4K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
20.4K
DNA Base Pairing02:27

DNA Base Pairing

31.2K
31.2K
DNA Base Pairing02:27

DNA Base Pairing

32.6K
Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
32.6K
DNA Isolation01:24

DNA Isolation

44.2K
DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
44.2K
DNA as a Genetic Template02:05

DNA as a Genetic Template

9.1K
9.1K

You might also read

Related Articles

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

Sort by
Same author

LegNER: a domain-adapted transformer for legal named entity recognition and text anonymization.

Frontiers in artificial intelligence·2025
Same author

Integrating Convolutional and Recurrent Neural Networks for Enhanced Medical Image Captioning.

Advances in experimental medicine and biology·2025
Same author

Enhanced Brain Tumor Classification with Convolutional Neural Networks.

Advances in experimental medicine and biology·2025
Same author

Leveraging Artificial Occluded Samples for Data Augmentation in Human Activity Recognition.

Sensors (Basel, Switzerland)·2025
Same author

Augmented reality in intensive care nursing education: A scoping review.

Nurse education in practice·2025
Same author

Artificial Intelligence Techniques in Grapevine Research: A Comparative Study with an Extensive Review of Datasets, Diseases, and Techniques Evaluation.

Sensors (Basel, Switzerland)·2024
Same journal

Peptidomics in the Spotlight: Advanced Sample Treatment Techniques and Analytical Insights.

Advances in experimental medicine and biology·2026
Same journal

Methods for the Investigation of Protein-Ligands Interactions.

Advances in experimental medicine and biology·2026
Same journal

Sample Preparation Strategies for Microbial Cell Surface Proteomics: Integrating Shaving and Shotgun Approaches.

Advances in experimental medicine and biology·2026
Same journal

Proteomic Sample Preparation for the Petroleum Industry: A Biocorrosion Case Study.

Advances in experimental medicine and biology·2026
Same journal

Proteomic and Functional Comparison of Extracellular Vesicles from Wild-Type and Lyn-Deficient Stromal Cells.

Advances in experimental medicine and biology·2026
Same journal

Proteomic Analysis of Histone Sequence Variants and Post-translationally Modified Forms.

Advances in experimental medicine and biology·2026
See all related articles

Related Experiment Video

Updated: Dec 20, 2025

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

15.6K

Apache Spark Implementations for String Patterns in DNA Sequences.

Andreas Kanavos1, Ioannis Livieris2, Phivos Mylonas3

  • 1Computer Engineering and Informatics Department, University of Patras, Patras, Greece. kanavos@ceid.upatras.gr.

Advances in Experimental Medicine and Biology
|May 30, 2020
PubMed
Summary
This summary is machine-generated.

This study explores Next-Generation Sequencing (NGS) data analysis using Apache Spark. Experiments focus on common bioinformatics problems like Longest Common Prefix, Substring, and Subsequence in genomic sequences.

Keywords:
DNA sequencingLongest Common Prefix (LCP)Longest Common Subsequence (LCS)Longest Common Substring

More Related Videos

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
08:53

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

776
Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

5.4K

Related Experiment Videos

Last Updated: Dec 20, 2025

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

15.6K
Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
08:53

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

776
Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

5.4K

Area of Science:

  • Bioinformatics and Computational Biology
  • Genomic Data Analysis
  • Cloud Computing in Genomics

Background:

  • The rapid increase in biological data, especially DNA sequences from Next-Generation Sequencing (NGS), presents significant analysis challenges.
  • Genomic research has been revolutionized by NGS technologies, generating vast amounts of sequence data.
  • Efficient computational frameworks are crucial for processing and analyzing large-scale genomic datasets.

Purpose of the Study:

  • To evaluate the performance of Apache Spark for analyzing Next-Generation Sequencing (NGS) data.
  • To investigate the application of cloud infrastructure in genomic data processing.
  • To address common sequence analysis problems including Longest Common Prefix, Longest Common Substring, and Longest Common Subsequence.

Main Methods:

  • Utilized Apache Spark, a cloud infrastructure framework, for data processing.
  • Conducted experiments on DNA sequences obtained from the National Center for Biotechnology Information (NCBI).
  • Implemented algorithms to find the Longest Common Prefix, Longest Common Substring, and Longest Common Subsequence.

Main Results:

  • Demonstrated the feasibility of using Apache Spark for analyzing large genomic datasets.
  • Provided experimental results for the performance of common sequence alignment algorithms on cloud infrastructure.
  • Successfully applied the framework to popular bioinformatics problems.

Conclusions:

  • Apache Spark offers a scalable and efficient platform for Next-Generation Sequencing (NGS) data analysis.
  • Cloud-based solutions are effective for tackling computational challenges in modern genomics.
  • The study highlights the importance of robust algorithms for sequence comparison in bioinformatics.