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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-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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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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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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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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An Integrated Approach for Microprotein Identification and Sequence Analysis
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UCSC Genome Browser enters 20th year.

Christopher M Lee1, Galt P Barber1, Jonathan Casper1

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

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The UCSC Genome Browser offers advanced genomics data visualization and annotation tools. Recent updates include a universal genome search, single-cell expression viewer, and new variation data displays for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The University of California Santa Cruz (UCSC) Genome Browser is a vital resource for the research community.
  • It has provided high-quality genomics data visualization and genome annotations for nearly 20 years.

Purpose of the Study:

  • To detail recent enhancements and new datasets added to the UCSC Genome Browser.
  • To highlight new features that improve data accessibility and visualization for genomic research.

Main Methods:

  • Development of new web tools, including a universal genome search for BLAT and a single-cell expression viewer.
  • Implementation of novel visualization modes like 'lollipop' plots for variation data.
  • Introduction of a RESTful API for data extraction and a custom-track backup feature.

Main Results:

  • Expanded search capabilities across all genomes via the web BLAT tool.
  • Launched a dedicated single-cell expression viewer at cells.ucsc.edu.
  • Integrated new datasets including Tabula Muris, GeneHancer, TCGA Pan-Cancer variants, GRC Patch sequences, ENCODE ChIP-seq data, DGVa Gold Standard Variants, and Genomenon Mastermind variants.
  • Added three new multi-species alignment tracks for comparative genomics.

Conclusions:

  • The UCSC Genome Browser continues to evolve, offering cutting-edge tools and comprehensive datasets.
  • These updates enhance the platform's utility for diverse genomic research applications, from single-cell analysis to variation studies.