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Sequence-Based Searching for SynBioHub Using VSEARCH.

Eric Yu1, Jeanet Mante2, Chris J Myers2

  • 1University of Utah, 201 Presidents' Circle, Salt Lake City, Utah 84112, United States.

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|January 21, 2022
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Summary
This summary is machine-generated.

SynBioHub now enables sequence-based part searching, allowing users to find biological parts by sequence. This new feature uses VSEARCH and SBOLExplorer for efficient and accurate part discovery.

Keywords:
PageRankSBOLSBOLExplorerSynBioHubUSEARCHVSEARCH

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Area of Science:

  • Synthetic Biology
  • Bioinformatics

Background:

  • Large biological part repositories require efficient search functionalities.
  • Previously, SynBioHub lacked a sequence-based search capability for its parts.

Purpose of the Study:

  • To integrate sequence-based searching into SynBioHub.
  • To enable users to find biological parts using sequence data.

Main Methods:

  • Integrated VSEARCH, an open-source global alignment tool, into SynBioHub.
  • Utilized SBOLExplorer, an open-source distributed search engine, for the core implementation.
  • Developed a novel scoring method for part similarity considering popularity and percentage match.

Main Results:

  • Sequence-based search is now available via SynBioHub's web interface and API.
  • Users can search using plain text or supported file formats for sequences.
  • The new scoring approach enhances the relevance of search results.

Conclusions:

  • The integration of sequence-based search significantly improves SynBioHub's utility.
  • This advancement facilitates more effective discovery and utilization of biological parts.
  • The developed methods contribute to better management of large biological part repositories.