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Related Concept Videos

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.
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
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...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: Jun 27, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical

Patrick J Killion1, Vishwanath R Iyer

  • 1Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, Texas 78712, USA. pkillion@mail.utexas.edu

Genome Biology
|November 19, 2008
PubMed
Summary
This summary is machine-generated.

ArrayPlex is a versatile software package designed for functional genomics research. It offers comprehensive tools for microarray data analysis, visualization, and genomic sequence retrieval, supporting researchers in their functional genomics studies.

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Introductory Analysis and Validation of CUT&RUN Sequencing Data
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Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Related Experiment Videos

Last Updated: Jun 27, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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Published on: December 22, 2017

Introductory Analysis and Validation of CUT&RUN Sequencing Data
04:58

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Functional genomics research generates large datasets requiring specialized software.
  • Existing tools may lack integration or comprehensive functionality for diverse analyses.

Purpose of the Study:

  • To introduce ArrayPlex, a unified software package for functional genomics.
  • To provide a flexible and extensible platform for various genomic data analyses.

Main Methods:

  • Development of a client-server architecture using open-source components.
  • Integration of diverse functional genomics toolsets including data storage, quality assessment, visualization, annotation, statistical testing, sequence retrieval, and motif analysis.
  • Provision of graphical, command-line, and programmatic access via a documented API.

Main Results:

  • ArrayPlex offers a centralized solution for multiple functional genomics tasks.
  • The software supports microarray data management and analysis.
  • It facilitates gene annotation, statistical analysis, and genomic sequence exploration.

Conclusions:

  • ArrayPlex provides a flexible, extensible, and comprehensive software solution for functional genomics.
  • Its integrated approach and multiple access methods enhance research efficiency.
  • The open-source package is readily available for the scientific community.