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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.
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...
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...

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Related Experiment Video

Updated: May 14, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Sequence assembly demystified.

Niranjan Nagarajan1, Mihai Pop

  • 1Computational and Systems Biology, Genome Institute of Singapore, 138672 Singapore.

Nature Reviews. Genetics
|January 30, 2013
PubMed
Summary
This summary is machine-generated.

Modern genome assembly methods are advancing rapidly due to new sequencing technologies. This review covers assembly foundations, practical trade-offs, and software for diverse applications like gene expression and metagenomics.

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Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology

Background:

  • Advances in DNA sequencing technologies and accessibility have spurred significant interest in sequence and genome assembly.
  • Emerging applications such as gene expression analysis, genomic variant discovery, and metagenomics present unique challenges and requirements for assembly.

Purpose of the Study:

  • To survey the theoretical underpinnings of contemporary genome assembly techniques.
  • To highlight practical considerations and trade-offs in assembly methods tailored for specific applications.
  • To review essential software tools and the relationship between experimental design and assembly effectiveness.

Main Methods:

  • Theoretical foundation review of sequence and genome assembly algorithms.
  • Analysis of assembly options and practical trade-offs.
  • Survey of key software tools and their applicability.
  • Examination of the interplay between experimental design and assembly outcomes.

Main Results:

  • Identification of diverse assembly needs across applications like gene expression, variant discovery, and metagenomics.
  • Evaluation of theoretical concepts underpinning modern assembly approaches.
  • Discussion of practical trade-offs influencing the choice of assembly methods and software.
  • Emphasis on the importance of experimental design for successful genome assembly.

Conclusions:

  • Understanding the theoretical basis and practical trade-offs of genome assembly is crucial for selecting appropriate methods and software.
  • Tailoring assembly strategies to specific applications, such as gene expression or metagenomics, is essential for maximizing data utility.
  • Effective experimental design significantly impacts the success and accuracy of sequence and genome assembly.