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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...
DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...

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Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Assembly of non-unique insertion content using next-generation sequencing.

Nathaniel Parrish1, Farhad Hormozdiari, Eleazar Eskin

  • 1Department of Computer Science, University of California Los Angeles, CA, USA.

BMC Bioinformatics
|October 13, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new computational method to identify and assemble both unique and repeated sequence insertions in the human genome. This advance improves our understanding of genomic variation and individual differences.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Sequence insertions significantly contribute to individual genomic variation.
  • Current methods struggle to identify and assemble repeated sequence insertions, limiting comprehensive analysis.
  • Most inserted sequences in the human genome are complex mixtures of unique and repeated elements.

Purpose of the Study:

  • To develop a computational method for discovering the content of sequence insertions, including unique, repeated, and mixed types.
  • To enable the characterization of previously unresolvable repeated sequence insertions.
  • To advance the study of genomic variation by providing tools for comprehensive insertion analysis.

Main Methods:

  • A novel computational approach analyzing paired-end read mappings and depth of coverage.
  • Identification of reads originating from inserted sequences, regardless of their repetitive nature.
  • Utilizing a segment extension technique to progressively assemble insertion content.

Main Results:

  • The method successfully identifies and assembles both unique and repeated sequence insertions.
  • Demonstrated reliable results in simulation studies using a modified mouse chromosome at 40x coverage.
  • Provides a framework for characterizing complex inserted sequences.

Conclusions:

  • The developed computational method offers a robust solution for discovering and assembling diverse sequence insertions.
  • This technique enhances the ability to study genomic variation driven by insertions.
  • Further application of this method can lead to a more complete understanding of the human genome.