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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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.
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Next-generation Sequencing03:00

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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.
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RNA-seq03:21

RNA-seq

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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. 
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Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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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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Sanger Sequencing01:57

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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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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.
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Updated: Aug 10, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis
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Microbial Genome Sequencing and Assembly Using Nanopore Sequencers.

Makoto Taniguchi1,2, Kazuma Uesaka3

  • 1Oral Microbiome Center, Taniguchi Dental Clinic, Kagawa, Japan. makoto@tani8020.jp.

Methods in Molecular Biology (Clifton, N.J.)
|February 13, 2023
PubMed
Summary
This summary is machine-generated.

Sequencing microbial genomes is now easier with long-read technologies like Oxford Nanopore. This guide details the experimental and computational methods for microbial genome sequencing and assembly.

Keywords:
Complete genomeGenome assemblyMicrobial genomesNanopore sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Microbiology

Background:

  • Microbial genomes are large DNA molecules, typically millions of base pairs.
  • Advances in sequencing technology have simplified genome analysis.
  • Long-read sequencing platforms offer improved assembly capabilities.

Purpose of the Study:

  • To describe the process of sequencing microbial genomes.
  • To outline the computational steps for assembling microbial genomes.
  • To provide a guide for researchers using long-read sequencing technologies.

Main Methods:

  • Experimental protocols for DNA extraction and library preparation.
  • Utilizing long-read sequencing platforms (e.g., Oxford Nanopore Technologies).
  • Bioinformatic pipelines for sequence assembly and quality control.

Main Results:

  • Successful sequencing and assembly of microbial genomes into single chromosomes.
  • Demonstration of the effectiveness of long-read sequencing for microbial genomics.
  • Detailed experimental and computational workflows.

Conclusions:

  • Long-read sequencing platforms significantly enhance microbial genome assembly.
  • The described methods provide a comprehensive approach to microbial genome analysis.
  • This chapter serves as a practical resource for microbial genomics research.