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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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.
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Next-generation Sequencing03:00

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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.
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Maxam-Gilbert Sequencing01:05

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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.
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Sanger Sequencing01:57

Sanger Sequencing

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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...
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RNA-seq03:21

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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. 
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Evolutionary Relationships through Genome Comparisons02:54

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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...
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Updated: Sep 8, 2025

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
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Current Progress in Phased Genome Assembly from Long-Read DNA Sequencing Data.

Jorge Ivan Diaz-Riaño1, Jorge Duitama2

  • 1Systems and computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.

Methods in Molecular Biology (Clifton, N.J.)
|July 30, 2025
PubMed
Summary
This summary is machine-generated.

This chapter details genome assembly algorithms, focusing on long-read sequencing for complex genomes. It covers data structures, scaffolding, phasing techniques, evaluation metrics, and specific tools like FALCON and HiCanu.

Keywords:
AlgorithmsGenome assemblyHaplotypeLong-reads SequencingPhasing Genomes

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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome assembly is fundamental to genomics, with long-read sequencing advancing complex genome construction and phasing.
  • Accurate genome assembly is crucial for understanding genetic variation and biological function.

Purpose of the Study:

  • To provide a comprehensive overview of algorithmic techniques for genome assembly, emphasizing phased assemblies.
  • To describe essential data structures, scaffolding methods, and evaluation metrics for high-quality genome construction.

Main Methods:

  • Review of overlap graphs and de Bruijn graphs for unphased assembly.
  • Description of trio data and Hi-C for long-range scaffolding and phasing.
  • Analysis of core algorithms in FALCON, HiCanu, Hifiasm, and NGSEP for phased assembly.

Main Results:

  • Detailed explanation of algorithmic approaches for both unphased and phased genome assembly.
  • Introduction to metrics for evaluating genome assembly completeness, accuracy, and base quality.
  • Comparison of key tools enabling high-quality phased genome construction.

Conclusions:

  • Algorithmic advancements, particularly with long-read technologies, have significantly improved phased genome assembly.
  • Understanding core data structures and phasing techniques is vital for utilizing modern genome assembly tools effectively.