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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.
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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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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis.

Sachin Mathur1, Mahesh Visvanathan, Stan Svojanovsky

  • 1School of Computing and Engineering, University of Missouri-Kansas City, MO 64110, USA.

The Open Bioinformatics Journal
|September 28, 2011
PubMed
Summary

We created GOAPhAR, a web tool integrating gene and protein data for microarray analysis. It aids researchers by providing functional pathways and statistical validation for gene clusters.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Microarray research generates large datasets requiring integrated analysis.
  • Accessing diverse biological information (annotations, pathways, interactions) is crucial for interpreting gene expression data.
  • Existing tools often lack comprehensive integration of these data types.

Purpose of the Study:

  • To develop a web-based tool, GOAPhAR (Gene Ontology, Annotations and Pathways for Array Research), for comprehensive analysis of microarray data.
  • To integrate diverse biological information sources into a single platform.
  • To provide tools for statistically validating gene expression clusters.

Main Methods:

  • Developed a web-based platform integrating Gene Ontology, annotations, pathways, protein interactions, and microarray datasets.
  • Implemented input options for Affymetrix probe IDs, Genbank, or Unigene identifiers for human, mouse, and rat genomes.
  • Incorporated statistical validation tools for microarray data clusters.

Main Results:

  • GOAPhAR successfully integrates disparate biological information relevant to microarray research.
  • The tool accepts multiple gene identifier types across key model organisms.
  • Results are presented in a user-friendly interface with direct links to information sources.

Conclusions:

  • GOAPhAR provides a valuable, integrated resource for researchers analyzing microarray data.
  • The platform simplifies the process of exploring gene functions, pathways, and interactions.
  • Facilitates statistically robust interpretation of gene expression patterns.