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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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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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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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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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Biostatistics plays a crucial role in understanding and analyzing data in healthcare and biology. Biostatisticians conduct experiments, gather evidence, and draw meaningful conclusions using statistical methods and techniques. Different variables form the foundation of biostatistical analysis, allowing researchers to understand and interpret data effectively. These variables are classified into different types, each serving a specific purpose in statistical analysis.
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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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JBrowse: a dynamic web platform for genome visualization and analysis.

Robert Buels1, Eric Yao1, Colin M Diesh2

  • 1Department of Bioengineering, University of California, Berkeley, California, USA.

Genome Biology
|April 14, 2016
PubMed
Summary
This summary is machine-generated.

JBrowse is a mature, fast genome visualization and analysis web application. It offers enhanced speed, scalability, and customization for complex genomic data, supporting both online and offline use.

Keywords:
BioinformaticsBrowserGenome

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • JBrowse is a JavaScript and HTML5-based genome browser.
  • It is designed for easy embedding into websites and applications or standalone use.

Purpose of the Study:

  • To present JBrowse as a mature web application for genome visualization and analysis.
  • To highlight its speed, scalability, and feature enhancements.

Main Methods:

  • Utilizes JavaScript and HTML5 for web-based genome browsing.
  • Incorporates a plugin framework for adding analysis functions.
  • Supports customization of track visuals, interactions, and data browsing.

Main Results:

  • Significant improvements in speed and scalability for handling large datasets.
  • Enhanced support for complex, interactive queries on extensive track sets.
  • Capabilities for offline browsing of local annotation files and generating publication-quality figures.

Conclusions:

  • JBrowse is a robust and mature web application.
  • It is well-suited for comprehensive genome visualization and analysis tasks.
  • The platform offers flexibility and advanced features for researchers.