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Related Concept Videos

Genomics02:02

Genomics

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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...
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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

Next-generation Sequencing

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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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Related Experiment Video

Updated: Feb 2, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing.

YongKiat Wee1, Salma Begum Bhyan1, Yining Liu2

  • 1School of Science and Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia.

Briefings in Functional Genomics
|November 22, 2018
PubMed
Summary

Third-generation sequencing (TGS) offers long reads for genomic analysis but has accuracy challenges. This study surveys 39 TGS tools, providing decision trees to guide researchers in selecting optimal software for de novo assembly and genome analysis.

Keywords:
genome assemblygenome sequencingmappingthird-generation sequencing

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Third-generation sequencing (TGS) enables detailed genomic analysis, including whole genome sequencing and de novo genome assembly.
  • TGS technology produces high-quality long reads, facilitating overlapping read determination and transcript isoform analysis.
  • Current TGS methods face challenges with nucleotide base accuracy and high error rates.

Purpose of the Study:

  • To survey and evaluate 39 third-generation sequencing (TGS)-related tools for de novo assembly and genome analysis.
  • To identify and compare the characteristics of these TGS tools, including input requirements, user interaction, sequencing platforms, read types, error models, coverage bias, variant simulation, and output formats.
  • To provide decision trees to assist researchers in selecting the most suitable tools for analyzing TGS data.

Main Methods:

  • Comprehensive survey of 39 TGS-related computational tools.
  • Comparative analysis of tool characteristics: input, user interaction, platforms, read types, error models, coverage bias, variant simulation, and outputs.
  • Development of decision trees for tool selection.

Main Results:

  • Detailed comparison of 39 TGS tools based on various computational features.
  • Identification of differences in error models, coverage bias potential, and variant simulation capabilities among tools.
  • Summary of tool characteristics to aid in data analysis.

Conclusions:

  • A comprehensive survey and evaluation of computational features for existing TGS analysis methods.
  • The study provides a valuable guideline for researchers navigating the landscape of TGS tools.
  • Decision trees are presented to facilitate the selection of appropriate tools for TGS data analysis, addressing accuracy and error rate challenges.