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Related Concept Videos

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.
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.
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...
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...
Oligosaccharide Assembly01:24

Oligosaccharide Assembly

Protein glycosylation starts in the ER lumen and continues in the Golgi apparatus. Glycosyltransferases catalyze the addition of sugar molecules or glycosylation of proteins. Usually, these enzymes add sugars to the hydroxyl groups of selected serine or threonine residues to form O-linked glycans or the amino groups of asparagine residues to form N-linked glycans. Different positions on the same polypeptide chain can contain differently linked glycans.
Multiple sugar molecules that may or may...

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Related Experiment Video

Updated: Jun 3, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Next generation sequence assembly with AMOS.

Todd J Treangen1, Dan D Sommer, Florent E Angly

  • 1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.

Current Protocols in Bioinformatics
|March 15, 2011
PubMed
Summary
This summary is machine-generated.

A Modular Open-Source Assembler (AMOS) provides tools for genome assembly, including de novo assemblers and scaffolders. This protocol details its use for Next Generation sequencing data, offering improved assembly quality for various datasets.

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Last Updated: Jun 3, 2026

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Published on: August 20, 2021

Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology

Background:

  • Genome assembly is crucial for understanding genetic information.
  • Existing tools may lack modularity or struggle with complex datasets.

Purpose of the Study:

  • To present a protocol for configuring and utilizing the A Modular Open-Source Assembler (AMOS).
  • To demonstrate AMOS's capabilities in assembling Next Generation sequence data.
  • To provide practical guidance for enhancing genome assembly quality.

Main Methods:

  • Utilizing the modular components of AMOS, including Minimus, Minimo, and Bambus 2.
  • Configuring AMOS for diverse sequencing data types.
  • Applying assembly strategies to bacterial, viral, and metagenomic datasets.

Main Results:

  • Successful configuration and application of AMOS for genome assembly.
  • Demonstration of Minimus, Minimo, and Bambus 2 for de novo assembly and scaffolding.
  • Identification of specific parameters and techniques to improve assembly quality.

Conclusions:

  • AMOS offers a flexible and powerful platform for genome assembly.
  • The protocol effectively guides users in applying AMOS to various genomic datasets.
  • AMOS facilitates high-quality genome assembly, particularly for complex and metagenomic data.