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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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Genome-wide Association Studies-GWAS01:11

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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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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Evolution of Microbial Genome01:08

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Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
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Genomic DNA in Eukaryotes00:58

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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.
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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The UCSC Genome Browser database: 2015 update.

Kate R Rosenbloom1, Joel Armstrong2, Galt P Barber2

  • 1Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA kate@soe.ucsc.edu.

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Summary
This summary is machine-generated.

The UCSC Genome Browser offers updated human genome assemblies and comparative genomics tools for researchers. It now features new species browsers, enhanced visualizations, and improved data sharing via hubs.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • The UCSC Genome Browser, established in 2001, serves as a vital resource for genome assemblies and annotations.
  • It supports scientists and students globally with comprehensive genomic data.

Purpose of the Study:

  • To detail recent advancements and expansions of the UCSC Genome Browser database and its associated tools.
  • To highlight new features, species data, and distribution mechanisms enhancing genomic research accessibility.

Main Methods:

  • Released the GRCh38 human genome reference assembly (UCSC hg38) with a new browser.
  • Developed a 100-species multiple alignment and conservation track for comparative genomics.
  • Introduced Genome Browser in a Box (GBiB) for novel distribution.
  • Created browsers for new species and expanded visualization options.
  • Increased public data hubs by threefold, supporting data sharing.

Main Results:

  • The UCSC Genome Browser now includes the GRCh38 human genome assembly and extensive comparative genomics data.
  • New browsers for Chinese hamster, elephant shark, and minke whale have been added.
  • Enhanced display features like stacked color graphs and region highlighting improve data interpretation.
  • The adoption of UCSC track and assembly hubs has significantly increased for data sharing.

Conclusions:

  • The UCSC Genome Browser continues to evolve as a leading resource for genomic information.
  • Recent updates enhance comparative genomics, data accessibility, and user-driven data sharing.
  • These advancements empower the scientific community with more comprehensive and user-friendly genomic tools.