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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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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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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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Genome Size and the Evolution of New Genes03:21

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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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Genome U-Plot: a whole genome visualization.

Athanasios Gaitatzes1,2, Sarah H Johnson1, James B Smadbeck1

  • 1Biomarker Discovery Program, Center for Individualized Medicine, Mayo Clinic.

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Summary
This summary is machine-generated.

The new Genome U-Plot visualizes whole genome sequencing data, improving the detection of structural variations. This novel layout enhances spatial resolution and readability for genomic analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Data Visualization

Background:

  • Whole genome sequencing (WGS) generates complex data, necessitating effective visualization tools.
  • Conventional 2D layouts for WGS data (circular, linear) have limitations in spatial efficiency.
  • Identifying structural variations (SVs) like deletions and amplifications requires clear graphical representation.

Purpose of the Study:

  • To introduce the Genome U-Plot, a novel visualization layout for WGS data.
  • To enhance the spatial resolution and aesthetic quality of genomic visualizations.
  • To facilitate the identification and analysis of structural variations in WGS data.

Main Methods:

  • Development of the Genome U-Plot, a layered, 2D layout for chromosome representation.
  • Quantitative comparison of Genome U-Plot with conventional visualization methods using metrics like line crossings.
  • Evaluation of visualization clarity and spatial resolution improvements.

Main Results:

  • The Genome U-Plot achieves significantly higher spatial resolution compared to traditional layouts.
  • The proposed visualization method improves graph readability by at least twofold.
  • The Genome U-Plot effectively displays SVs, aiding in the identification of genomic alterations.

Conclusions:

  • The Genome U-Plot offers a more efficient and intuitive way to visualize WGS data.
  • This tool enables researchers to gain novel insights into structural variations.
  • The improved visualization facilitates hypothesis generation and identification of genomic changes.