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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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...
Genomics02:02

Genomics

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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Genomic DNA in Eukaryotes

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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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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An Integrated Approach for Microprotein Identification and Sequence Analysis
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Published on: July 12, 2022

ENCODE whole-genome data in the UCSC Genome Browser: update 2012.

Kate R Rosenbloom1, Timothy R Dreszer, Jeffrey C Long

  • 1Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA. kate@soe.ucsc.edu

Nucleic Acids Research
|November 15, 2011
PubMed
Summary

The Encyclopedia of DNA Elements (ENCODE) project provides comprehensive functional annotations for the human and mouse genomes. This resource offers extensive data from diverse cell types and biochemical assays for public research.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • The Encyclopedia of DNA Elements (ENCODE) Consortium is a major international research effort.
  • ENCODE aims to identify all functional elements in the human genome.

Purpose of the Study:

  • To report on the progress and current state of the ENCODE project's functional genomics data generation and dissemination.
  • To highlight the expansion of ENCODE's data compendium in terms of assays, cell types, and species coverage.

Main Methods:

  • Utilizing a diverse set of 27 biochemical assays across numerous human and mouse cell types.
  • Generating high-quality, whole-genome functional annotations.
  • Completing and submitting over 2000 individual experiments for public access.

Main Results:

  • ENCODE has reached a critical mass of functional elements data for the human genome, covering 200 cell types.
  • Mouse genome functional elements are also being studied, with data from 37 cell types.
  • Extensive data is publicly available through the UCSC Genome Browser and ENCODE portal.

Conclusions:

  • The ENCODE project has significantly advanced whole-genome functional annotation.
  • The comprehensive dataset is readily accessible for research, facilitating further genomic studies.
  • Continued data generation and public dissemination are key to ENCODE's mission.