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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.
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
DNA Packaging00:58

DNA Packaging

Overview
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...
Chromatin Packaging01:32

Chromatin Packaging

Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
Chromatin Packaging02:21

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.

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Related Experiment Video

Updated: Jun 5, 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

Succinct data structures for assembling large genomes.

Thomas C Conway1, Andrew J Bromage

  • 1NICTA Victoria Research Laboratory, Department of Computer Science and Engineering, The University of Melbourne, Parkville, Australia. tom.conway@nicta.com.au

Bioinformatics (Oxford, England)
|January 20, 2011
PubMed
Summary
This summary is machine-generated.

Researchers developed a new method for de novo genome assembly using succinct data structures to significantly reduce memory requirements. This breakthrough enables more efficient analysis of complex genomes, including human biomedicine applications.

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Related Experiment Videos

Last Updated: Jun 5, 2026

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

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Published on: August 20, 2021

Metagenomic Analysis of Silage
08:43

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Published on: January 13, 2017

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Second-generation sequencing enables de novo assembly of complex genomes.
  • De novo assembly is crucial for understanding biological variation and human biomedicine.
  • Current computational tools face challenges due to complexity and memory demands.

Purpose of the Study:

  • To address computational limitations in de novo genome assembly.
  • To develop a more memory-efficient representation for de Bruijn graphs.
  • To improve the feasibility of assembling higher eukaryotic genomes.

Main Methods:

  • Utilized entropy compressed or succinct data structures for de Bruijn graph representation.
  • Developed a novel approach to reduce storage requirements for assembly graphs.
  • Implemented and tested the method on a human genome proof-of-concept assembly.

Main Results:

  • Achieved at least a 10-fold reduction in storage compared to existing methods.
  • Demonstrated improved asymptotic scaling behavior in the presence of sequencing errors.
  • Successfully performed a proof-of-concept human genome assembly on a modest server.

Conclusions:

  • Succinct data structures offer a practical and efficient solution for de novo genome assembly.
  • The developed method significantly lowers memory requirements, making complex genome analysis more accessible.
  • This advancement has implications for large-scale structural and fine-scale sequence variation studies.