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Related Concept Videos

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Some researchers gain access to large amounts of data without interacting with a single research participant. Instead, they use existing records to answer various research questions. This type of research approach is known as archival research. Archival research relies on looking at past records or data sets to look for interesting patterns or relationships. For example, a researcher might access the academic records of all individuals who enrolled in college within the past ten years and...
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Related Experiment Video

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Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
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Computational approaches to mine publicly available databases.

Rodger B Voelker1, William A Cresko, J Andrew Berglund

  • 1Institutes of Molecular Biology and Ecology and Evolution, University of Oregon, Eugene, OR, USA.

Methods in Molecular Biology (Clifton, N.J.)
|February 20, 2014
PubMed
Summary
This summary is machine-generated.

This chapter introduces publicly available sequence annotation data, including structural and functional annotations. It details how to access, manipulate, and interrogate this data, using a ChIP-seq example for Next-Gen sequencing analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Publicly available sequence annotation data is crucial for biological research, providing structural and functional information on genomic features.
  • Annotation data aids in the analysis of Next-Generation sequencing data, such as identifying genomic features associated with mapped reads.
  • Efficiently obtaining, manipulating, and interrogating annotation data is an essential skill for researchers.

Purpose of the Study:

  • To introduce researchers to primary data repositories for sequence annotations.
  • To describe common file formats used for annotation data.
  • To demonstrate practical applications of annotation data through a worked example.

Main Methods:

  • Introduction to key data repositories for genomic annotations.
  • Explanation of commonly encountered file formats for sequence annotation data.
  • A fully worked example using annotation data to analyze a ChIP-seq dataset.

Main Results:

  • Researchers can leverage public annotation data for various analyses.
  • Understanding data formats and repositories facilitates efficient data retrieval and manipulation.
  • A practical ChIP-seq example illustrates the utility of annotation data in answering biological questions.

Conclusions:

  • Publicly available sequence annotation data is a vital and empowering resource for biological discovery.
  • The ability to work with annotation data enhances the interrogation of Next-Generation sequencing data.
  • This chapter equips researchers with the foundational knowledge and practical skills to utilize annotation data effectively.