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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.
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...
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.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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...

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Related Experiment Video

Updated: May 14, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Genome reassembly with high-throughput sequencing data.

Nathaniel Parrish1, Benjamin Sudakov, Eleazar Eskin

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

BMC Genomics
|February 2, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a novel computational method that integrates reference genomes into de novo assembly, significantly improving structural variation detection. This approach bridges the gap between existing genome assembly and resequencing techniques.

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Novel Sequence Discovery by Subtractive Genomics
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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Related Experiment Videos

Last Updated: May 14, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Structural variations are key to individual differences in genomics.
  • Current methods for structural variation detection are either de novo assembly or resequencing-based.
  • A gap exists between de novo assembly and resequencing methods for structural variation analysis.

Purpose of the Study:

  • To present a computational method for integrating reference sequences into genome assembly.
  • To improve the accuracy and efficiency of structural variation identification.
  • To bridge the gap between de novo assembly and resequencing approaches.

Main Methods:

  • Developed a novel graph construction based on the de Bruijn graph, incorporating reference sequences.
  • Implemented an iterative message-passing algorithm to leverage reference information for assembly.
  • Validated the method on simulated 5 Mb genomes from mammalian and bacterial references.

Main Results:

  • The proposed method significantly improves genome assembly results by incorporating reference data.
  • Demonstrated effectiveness on both mammalian and bacterial simulated genomes.
  • Provided a discussion on the benefits and limitations of the reference-guided assembly technique.

Conclusions:

  • Reference-guided assembly offers a powerful approach to enhance structural variation detection.
  • The novel graph construction and message-passing algorithm effectively improve assembly.
  • This method represents a significant step towards bridging assembly and resequencing.