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Novel Sequence Discovery by Subtractive Genomics
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Computational prospecting the great viral unknown.

Bonnie L Hurwitz1, Jana M U'Ren2, Ken Youens-Clark2

  • 1Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA bhurwitz@email.arizona.edu.

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|April 1, 2016
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Summary
This summary is machine-generated.

Bacteriophages, or phages, are crucial in regulating bacterial populations and host metabolism. New computational methods for analyzing viral metagenomes (viromes) reveal phage functions, even for unknown viral genes.

Keywords:
bacteriophagebioinformaticsmetagenomicsphageviromevirus

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Bacteriophages influence bacterial populations and host metabolism through gene transfer and expression.
  • Metagenomics, particularly viral metagenomics (viromes), offers insights into phage auxiliary metabolic genes (AMGs) that reprogram host metabolism.
  • A significant portion of virome sequences lack matches to known proteins, highlighting the need for advanced analytical tools.

Purpose of the Study:

  • To provide an overview of current computational methodologies for virome analysis.
  • To present reference-independent approaches for examining viromes, including human skin viromes.
  • To introduce methods for validating auxiliary metabolic genes (AMGs) and mitigating host contamination.

Main Methods:

  • Utilizing reference-independent computational techniques like protein clustering, contig spectra, and ecological profiling.
  • Applying these methods to analyze human skin viromes.
  • Developing and presenting strategies for validating auxiliary metabolic genes (AMGs) against host contamination.

Main Results:

  • Demonstrated the utility of reference-independent computational methods in virome analysis.
  • Provided insights into the diversity and functional roles of phages in various environments.
  • Successfully applied methods to validate auxiliary metabolic genes (AMGs) in human skin viromes.

Conclusions:

  • Computational advancements are essential for understanding the known and unknown components of viromes.
  • Reference-independent approaches offer novel insights into phage diversity and function.
  • Accurate validation of auxiliary metabolic genes (AMGs) is crucial for understanding phage-host interactions.