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Related Concept Videos

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.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

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Related Experiment Video

Updated: Jun 5, 2026

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

Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing.

Mattia C F Prosperi1, Luciano Prosperi, Alessandro Bruselles

  • 1Clinic of Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy. ahnven@yahoo.it

BMC Bioinformatics
|January 7, 2011
PubMed
Summary
This summary is machine-generated.

This study presents a new algorithm for reconstructing viral quasispecies from next-generation sequencing (NGS) data, improving the analysis of intra-host evolution and viral variants. The method effectively identifies true variants and minimizes false ones, even with sequencing errors.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Related Experiment Videos

Last Updated: Jun 5, 2026

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

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Area of Science:

  • Genomics
  • Virology
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) enables high-throughput genomics but reconstructing viral quasispecies remains challenging.
  • Analyzing intra-host viral evolution requires accurate reconstruction of complex viral populations.
  • Current methods struggle with the nuances of viral quasispecies, particularly in relation to immune responses and therapies.

Purpose of the Study:

  • To develop a novel algorithm for viral quasispecies reconstruction using NGS data.
  • To provide formulae for combinatorial analysis of quasispecies.
  • To minimize the reconstruction of false variants (in-silico recombinants).

Main Methods:

  • Developed a reconstruction algorithm based on combinations of multinomial distributions.
  • Utilized a reference genome partitioned into sliding windows (amplicons).
  • Applied combinatorial analysis to assess reconstruction difficulty and population diversity.

Main Results:

  • The algorithm accurately reconstructed true variants from simulated data, even at low genetic diversity.
  • Demonstrated effectiveness on empirical NGS data from hepatitis B virus patients.
  • Successfully characterized distinct viral variants from different patients.

Conclusions:

  • Combinatorial analysis quantifies the challenges in quasispecies reconstruction based on amplicon partitioning and diversity.
  • The developed algorithm shows robust performance on both simulated and real-world NGS data.
  • The method is effective even when accounting for sequencing errors.