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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.
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.
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...
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...
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...
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...

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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

Next-generation sequencing technologies and fragment assembly algorithms.

Heewook Lee1, Haixu Tang

  • 1School of Informatics and Computing, Indiana University, Bloomington, IN, USA.

Methods in Molecular Biology (Clifton, N.J.)
|March 13, 2012
PubMed
Summary
This summary is machine-generated.

This review covers DNA fragment assembly algorithms, from classic methods to new approaches for next-generation sequencing (NGS). It highlights challenges and emerging problems in assembling NGS data.

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06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Fragment assembly is a long-standing bioinformatics challenge.
  • Next-generation sequencing (NGS) technologies have accelerated DNA sequencing but introduced new assembly complexities.
  • NGS data is characterized by shorter reads, higher error rates, and significantly higher throughput.

Purpose of the Study:

  • To review classic and contemporary algorithms for DNA fragment assembly.
  • To focus on assembly strategies tailored for next-generation sequencing data.
  • To explore novel assembly problems arising from broader NGS applications.

Main Methods:

  • Review of established fragment assembly algorithms.
  • Analysis of algorithms developed for next-generation sequencing data.
  • Discussion of emerging assembly challenges distinct from traditional fragment assembly.

Main Results:

  • Classic fragment assembly methods face limitations with NGS data.
  • New algorithms are adapting to the characteristics of NGS reads (shorter length, higher error rate, high throughput).
  • NGS applications introduce unique assembly problems beyond the scope of classic approaches.

Conclusions:

  • The field of fragment assembly has evolved significantly due to NGS advancements.
  • Adaptation of algorithms is crucial for efficient and accurate assembly of NGS data.
  • Future research directions include addressing new assembly challenges posed by expanding NGS applications.