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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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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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.
GWAS does not require the identification of the target gene involved in...
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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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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: 2021 update.

Jairo Navarro Gonzalez1, Ann S Zweig1, Matthew L Speir1

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

Nucleic Acids Research
|November 22, 2020
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Summary
This summary is machine-generated.

The UCSC Genome Browser offers advanced genomics data visualization and annotation tools. Recent updates enhance data display and incorporate new gene annotations and regulatory element tracks.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Data Visualization

Background:

  • The UCSC Genome Browser has been a vital resource for genomics data visualization and annotation for over 20 years.
  • The rapidly expanding field of genomics necessitates continuous updates to data display and annotation capabilities.

Purpose of the Study:

  • To introduce new features and data tracks for the UCSC Genome Browser, enhancing its utility for researchers.
  • To maintain the database with up-to-date gene annotations and incorporate emerging genomic data.

Main Methods:

  • Implementation of new visualization modes, including Hi-C heatmap and phased family trio displays.
  • Integration of updated gene annotations from GENCODE, NCBI RefSeq, and Ensembl.
  • Addition of new data tracks for human and mouse genomes, such as ENCODE candidate cis-regulatory elements and Eukaryotic Promoter Database promoters.

Main Results:

  • The UCSC Genome Browser now features enhanced visualization tools like Hi-C heatmaps and phased trio displays.
  • Updated gene annotations (GENCODE, RefSeq, Ensembl) and new tracks (ENCODE, EP D, MANE) are available.
  • A dedicated SARS-CoV-2 genome browser was rapidly developed and released.

Conclusions:

  • The UCSC Genome Browser continues to evolve, providing researchers with cutting-edge tools for genomic data analysis.
  • The integration of new features and data ensures the browser remains a comprehensive and up-to-date resource.
  • The rapid deployment of a SARS-CoV-2 browser highlights the platform's adaptability and responsiveness to urgent research needs.