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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 Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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...
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...

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Related Experiment Video

Updated: Jul 8, 2026

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

Metagenomics: read length matters.

K Eric Wommack1, Jaysheel Bhavsar, Jacques Ravel

  • 1Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, Delaware 19711,USA.

Applied and Environmental Microbiology
|January 15, 2008
PubMed
Summary
This summary is machine-generated.

Short pyrosequencing reads are insufficient for comprehensive microbial metagenomic analysis. These short sequences miss distant gene homologs and reduce functional diversity detection, limiting their use in microbial community characterization.

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Last Updated: Jul 8, 2026

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

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Published on: March 15, 2019

Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

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

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Metagenomic analysis aims to understand microbial community phylogenetic and functional diversity.
  • Advancements in sequencing technologies like 454 pyrosequencing have lowered costs, making metagenomics more accessible.
  • Short sequence reads (100-200 bp) from pyrosequencing are being considered for metagenomic applications.

Purpose of the Study:

  • To evaluate the suitability of short pyrosequencing reads for phylogenetic and functional characterization of microbial communities.
  • To compare the efficacy of short reads versus long reads in metagenomic analysis using BLAST and COG analyses.

Main Methods:

  • Comparison of BLASTX and COG analyses between long (approx. 750 bp) and short (approx. 100-200 bp) sequence reads from microbial and virioplankton metagenome libraries.
  • Evaluation of increased short-read sampling depth and read length (up to 400 bp).

Main Results:

  • Short reads detected significantly fewer homologs via BLASTX compared to long reads, particularly for virioplankton.
  • Distant gene homologs were largely missed by short reads; only close homologs were detected.
  • Short reads missed up to 72% of COG hits identified by long reads, even with increased sampling depth.

Conclusions:

  • Short-read pyrosequencing data is currently inadequate for comprehensive metagenomic characterization of microbial communities.
  • Limitations in computational analysis for short sequences further hinder their utility.
  • Longer reads or alternative methods are recommended for accurate phylogenetic and functional profiling.