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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.
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Genetic Variation01:25

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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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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 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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Related Experiment Video

Updated: Mar 30, 2026

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe
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The Saccharomyces Genome Database Variant Viewer.

Travis K Sheppard1, Benjamin C Hitz1, Stacia R Engel1

  • 1Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

Nucleic Acids Research
|November 19, 2015
PubMed
Summary

The Saccharomyces Genome Database (SGD) now offers the Variant Viewer, a tool for visualizing genomic differences in Saccharomyces cerevisiae strains. This open-source application aids in analyzing sequence variation and allelic differences across multiple yeast genomes.

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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Area of Science:

  • Genomics
  • Bioinformatics
  • Yeast Biology

Background:

  • The Saccharomyces Genome Database (SGD) is a key resource for Saccharomyces cerevisiae research.
  • Increasing availability of diverse S. cerevisiae genomes necessitates advanced analysis tools.
  • Previous resources lacked comprehensive visualization of genomic and proteomic variations.

Purpose of the Study:

  • To introduce the Variant Viewer, a novel web application for visualizing genomic and proteomic differences.
  • To provide a dynamic platform for exploring sequence variation and allelic differences within S. cerevisiae.
  • To enhance the analysis of multiple S. cerevisiae strain genomes.

Main Methods:

  • Development of a dynamic, open-source web application named Variant Viewer.
  • Construction of multiple sequence alignments for 11 high-quality S. cerevisiae genome sequences.
  • Encoding of alignments and summaries in JSON format for efficient data handling.

Main Results:

  • The Variant Viewer enables dynamic, two-tiered visualization of the budding yeast pan-genome.
  • The application integrates sequence variation and allelic data from multiple S. cerevisiae strains.
  • The tool is accessible via the Saccharomyces Genome Database website.

Conclusions:

  • The Variant Viewer significantly enhances the ability to study genomic diversity in Saccharomyces cerevisiae.
  • This tool facilitates comparative genomics and the analysis of allelic differences.
  • The open-source nature promotes community engagement and further development in yeast genomics.