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

Next-generation Sequencing03:00

Next-generation Sequencing

94.3K
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....
94.3K
Improving Translational Accuracy02:07

Improving Translational Accuracy

12.0K
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...
12.0K
RNA-seq03:21

RNA-seq

10.6K
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...
10.6K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

11.7K
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...
11.7K

You might also read

Related Articles

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

Sort by
Same author

MetagenomicKG: a knowledge graph for metagenomic applications.

Bioinformatics (Oxford, England)·2026
Same author

Challenges and recommendations in establishing national human diversity genomic projects.

Nature methods·2026
Same author

Pathogen-specific host responses define distinct pneumonia endotypes in the human lung.

bioRxiv : the preprint server for biology·2026
Same author

Mitochondrial L-2-hydroxyglutarate is a physiological signalling metabolite.

Nature·2026
Same author

FastGxC: Fast and powerful context-specific eQTL mapping in bulk and single-cell data.

Cell genomics·2026
Same author

Towards a decentralized future for open-science databases.

Nature genetics·2026
Same journal

Integrated lipidomic and transcriptomic profiling of the host response in human malaria.

Genome biology·2026
Same journal

Centromeric satellite expansion drives genome evolution in the snowy owl.

Genome biology·2026
Same journal

Mapping the landscape of allele-specific expression in porcine genomes.

Genome biology·2026
Same journal

Genomic sequence evolution underlying human neocortical interareal diversification.

Genome biology·2026
Same journal

Regulatory mechanisms driven by functional 3'-UTR variants in alcohol use disorder and related traits.

Genome biology·2026
Same journal

A longitudinal single-nucleus transcriptomic atlas of bovine placentation reveals dynamic cellular hierarchies and regulatory programs.

Genome biology·2026
See all related articles

Related Experiment Video

Updated: Oct 22, 2025

Large-area Scanning Probe Nanolithography Facilitated by Automated Alignment and Its Application to Substrate Fabrication for Cell Culture Studies
09:45

Large-area Scanning Probe Nanolithography Facilitated by Automated Alignment and Its Application to Substrate Fabrication for Cell Culture Studies

Published on: June 12, 2018

9.8K

Technology dictates algorithms: recent developments in read alignment.

Mohammed Alser1,2,3, Jeremy Rotman4, Dhrithi Deshpande5

  • 1Computer Science Department, ETH Zürich, 8092, Zürich, Switzerland.

Genome Biology
|August 27, 2021
PubMed
Summary
This summary is machine-generated.

This study surveys 107 read alignment algorithms for genomic analysis, evaluating 11 methods to show how different algorithms impact sequencing read alignment speed and efficiency.

More Related Videos

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

23.2K
Collection and Extraction of Saliva DNA for Next Generation Sequencing
06:58

Collection and Extraction of Saliva DNA for Next Generation Sequencing

Published on: August 27, 2014

39.6K

Related Experiment Videos

Last Updated: Oct 22, 2025

Large-area Scanning Probe Nanolithography Facilitated by Automated Alignment and Its Application to Substrate Fabrication for Cell Culture Studies
09:45

Large-area Scanning Probe Nanolithography Facilitated by Automated Alignment and Its Application to Substrate Fabrication for Cell Culture Studies

Published on: June 12, 2018

9.8K
Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

23.2K
Collection and Extraction of Saliva DNA for Next Generation Sequencing
06:58

Collection and Extraction of Saliva DNA for Next Generation Sequencing

Published on: August 27, 2014

39.6K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Read alignment is a critical step in genomic analysis.
  • Advancements in sequencing technology have driven the development of diverse computational alignment algorithms.
  • Understanding these algorithms is key to efficient genomic data processing.

Purpose of the Study:

  • To systematically survey algorithmic foundations and methodologies of 107 read alignment methods for short and long reads.
  • To experimentally evaluate the performance of 11 selected read aligners.
  • To discuss the adaptation of alignment algorithms for specific biological domains.

Main Methods:

  • Comprehensive literature review and systematic survey of 107 read alignment algorithms.
  • Rigorous experimental evaluation of 11 representative read aligners.
  • Comparative analysis of algorithm impact on speed and efficiency.

Main Results:

  • A systematic overview of algorithmic approaches in read alignment is presented.
  • Experimental results demonstrate significant variations in speed and efficiency among different aligners.
  • The influence of underlying algorithms on alignment performance is quantified.

Conclusions:

  • The choice of read alignment algorithm significantly affects genomic analysis pipeline performance.
  • This survey provides a foundation for selecting appropriate alignment tools.
  • Tailoring alignment strategies is crucial for diverse biological applications.