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Genomics02:02

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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-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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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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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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An Integrated Approach for Microprotein Identification and Sequence Analysis
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The UCSC Genome Browser database: 2017 update.

Cath Tyner1, Galt P Barber2, Jonathan Casper2

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

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Summary
This summary is machine-generated.

The UCSC Genome Browser offers a free, open-source platform for visualizing genomic data. Recent updates enhance its usability and expand support for new species and data types, aiding biomedical research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The University of California, Santa Cruz (UCSC) Genome Browser has been a vital resource since 2001.
  • It provides a web-based, open-source platform for displaying genomic sequence alignments and annotations.
  • The platform supports a vast collection of reference genome assemblies.

Purpose of the Study:

  • To detail recent enhancements and new features of the UCSC Genome Browser.
  • To highlight the continuous support provided to the genomics and biomedical research communities.
  • To showcase the expansion of the platform's capabilities and accessibility.

Main Methods:

  • Web-based platform development and maintenance.
  • Integration of new genome assemblies and data types.
  • Enhancement of graphical user interfaces and data query tools.

Main Results:

  • Newly designed home and gateway pages for improved user experience.
  • Introduction of a 'multi-region' track display for versatile visualization.
  • Addition of genome browsers for three new species and updates to eight existing assemblies.
  • Extended support for data types including CRAM, RNA-seq, and chromatin interaction pairs.
  • Establishment of a new supported mirror site in Japan.

Conclusions:

  • The UCSC Genome Browser continues to evolve, offering enhanced tools and broader support for genomic research.
  • These updates improve data accessibility and visualization capabilities for the international scientific community.
  • The platform remains a cornerstone for bioinformatics, facilitating complex genomic data analysis.