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

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...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...

You might also read

Related Articles

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

Sort by
Same author

Real-time, automated, standardized, and transparent analysis of microfluidic nanoparticle data with RPSPASS.

bioRxiv : the preprint server for biology·2026
Same author

Alveolar niche disruption and aberrant epithelial reprogramming are early hallmarks of idiopathic pulmonary fibrosis.

bioRxiv : the preprint server for biology·2026
Same author

Circadian Homeostasis of Liver Metabolism Suppresses Hepatocarcinogenesis.

Cancer cell·2026
Same author

Molecular Mechanisms Underlying Recurrent Discrete Subaortic Stenosis: Insights from Bioinformatics Analysis of Human Tissue Samples.

The Annals of thoracic surgery·2026
Same author

Early Pulmonary Fibrosis is Defined by Niche- and Cell-Specific Molecular Programs.

bioRxiv : the preprint server for biology·2026
Same author

Authors' response.

Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology·2026
Same journal

Trust, Reproducibility, and Progress: The Roles of Independent Blind Prediction and Assessment and Benchmarking in Computational Biology.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

The Evolving Cyberinfrastructure at the National Institutes of Health to Support Data and AI in Biomedical Research.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

Applications of AI & ML in Biomanufacturing of Cell and Gene Therapies.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

AI for Health: Leveraging Artificial Intelligence to Revolutionize Healthcare.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

Workshop Introduction: Advances of AI Methods in Single Cell Spatial Omics.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

DRIVE-KG: Enhancing variant-phenotype association discovery in understudied complex diseases using heterogeneous knowledge graphs.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
See all related articles

Related Experiment Video

Updated: Jun 23, 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

Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies.

Cristian Coarfa1, Aleksandar Milosavljevic

  • 1Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|January 31, 2008
PubMed
Summary
This summary is machine-generated.

Pash 2.0 enhances sequence anchoring accuracy and speed using multi-diagonal gapped kmer collation. This method is effective for human resequencing and anchoring across close evolutionary distances.

More Related Videos

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
10:24

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
11:26

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Related Experiment Videos

Last Updated: Jun 23, 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

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
10:24

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
11:26

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) requires anchoring sequence fragments to reference genomes.
  • High-volume anchoring is crucial for large-scale genomic analyses.

Purpose of the Study:

  • To introduce improvements in the Positional Hashing method (Pash 2.0) for enhanced anchoring accuracy and speed.
  • To demonstrate the efficacy of gapped kmer matching for anchoring across close evolutionary distances, including human resequencing.

Main Methods:

  • Implementation of multi-diagonal gapped kmer collation in Pash 2.0.
  • Development of a novel benchmark for evaluating anchoring program performance, considering genomic duplicative structures.
  • Comparison of Pash 2.0 performance against BLAT in large-scale anchoring experiments.

Main Results:

  • Pash 2.0 achieves significant speedups, up to tenfold, compared to BLAT.
  • Multi-diagonal gapped kmer collation improves both accuracy and speed of Positional Hashing.
  • The proposed benchmark effectively captures key performance parameters for anchoring programs.

Conclusions:

  • Gapped kmer matching with cross-diagonal collation is sufficient for anchoring in scenarios with close evolutionary distances, such as human resequencing.
  • Pash 2.0 offers a substantial performance improvement for high-volume sequence anchoring tasks.
  • The developed benchmark provides a standardized method for assessing anchoring tool performance.