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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

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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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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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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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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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The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...
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Updated: Jan 11, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
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The UCSC Genome Browser database: 2026 update.

Jonathan Casper1, Matthew L Speir1, Brian J Raney1

  • 1Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, United States.

Nucleic Acids Research
|November 18, 2025
PubMed
Summary
This summary is machine-generated.

The UCSC Genome Browser offers updated tools for comparing genome annotations. New features include a heatmap for mutation data, QuickLift for assembly data transfer, and HubSpace for simplified track hub creation.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The UCSC Genome Browser has been a key resource for 25 years.
  • Researchers require tools to visualize and compare genomic annotations across different assemblies.

Purpose of the Study:

  • To introduce significant updates to the UCSC Genome Browser.
  • To enhance data visualization, data transfer, and track hub management for researchers.

Main Methods:

  • Implemented a positional heatmap display for mutation consequence data from MaveDB.
  • Developed QuickLift for copying annotation data between genome assemblies.
  • Introduced HubSpace to streamline track hub creation and usage with dedicated storage.

Main Results:

  • A new heatmap visualization is available for functional mutation data.
  • QuickLift enables efficient annotation data transfer across related assemblies.
  • HubSpace simplifies track hub management, offering dedicated user storage.

Conclusions:

  • The updated UCSC Genome Browser provides enhanced capabilities for genomic data analysis and sharing.
  • New features improve the visualization of mutation consequences and the management of genomic annotations.