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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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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 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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CRISPR/Cas9 Genome Editing01:28

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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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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: 2018 update.

Jonathan Casper1, Ann S Zweig1, Chris Villarreal1

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

Nucleic Acids Research
|November 7, 2017
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Summary
This summary is machine-generated.

The UCSC Genome Browser offers an updated web interface for exploring genome assemblies and annotation tracks. Recent enhancements include CRISPR/Cas9 support and improved variant analysis tools for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • The UCSC Genome Browser is a vital resource for exploring annotated genome assemblies.
  • Continuous updates are essential for maintaining the relevance and utility of genomic databases.

Purpose of the Study:

  • To report on recent updates and new features of the UCSC Genome Browser.
  • To highlight improvements in data visualization and analysis tools for genomic research.

Main Methods:

  • Web interface development and data integration.
  • Implementation of new annotation tracks and analysis tools.
  • User feedback incorporation for iterative improvements.

Main Results:

  • Addition of 12 new genome assemblies and over 28 annotation tracks in the past year.
  • Introduction of CRISPR/Cas9 guide sequence display and an interactive gene interaction navigator.
  • Upgrades include a command-line Variant Annotation Integrator and enhanced highlighting capabilities.

Conclusions:

  • The UCSC Genome Browser continues to evolve, providing researchers with cutting-edge tools for genome exploration.
  • Recent updates enhance the browser's utility for diverse genomic analyses, including CRISPR applications and variant interpretation.