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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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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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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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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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GenArk: towards a million UCSC genome browsers.

Hiram Clawson1, Brian T Lee2, Brian J Raney2

  • 1Genomics Institute, University of California, Santa Cruz, CA, 95064, USA. hclawson@ucsc.edu.

Genome Biology
|October 2, 2023
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Summary
This summary is machine-generated.

The Genome Archive (GenArk) collection provides fast visualization of recent NCBI genome assemblies using UCSC Genome Browsers. This resource enables rapid access to genomic data and annotations for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Interactive graphical genome browsers are vital for genomics research.
  • Existing browsers often lack comprehensive and up-to-date genome assemblies.
  • Access to diverse and recent genome assemblies is crucial for comprehensive analysis.

Purpose of the Study:

  • To create a collection of UCSC Genome Browsers for recent NCBI genome assemblies.
  • To enable fast and efficient visualization of genomic annotations.
  • To provide a platform for integrating diverse genomic datasets.

Main Methods:

  • Developed the Genome Archive (GenArk) collection using the UCSC Genome Browser framework.
  • Utilized an established track hub system for efficient data integration and visualization.
  • Implemented bulk import capabilities for third-party resources, including gene models and repeat masks.

Main Results:

  • Successfully integrated 3,269 NCBI genome assemblies into the GenArk collection.
  • Enabled fast visualization of gene models, repeat masks, BLAT alignments, and in silico PCR results.
  • Demonstrated the ability to incorporate external data, such as TOGA and Ensembl gene models.

Conclusions:

  • GenArk significantly enhances access to recent genome assemblies for visualization and analysis.
  • The track hub system facilitates rapid integration of diverse genomic annotations.
  • This resource empowers researchers with a more complete view of genomic data.