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Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data.

William H Thiel1

  • 1Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA; François M. Abboud Cardiovascular Research Center, University of Iowa, Iowa City, Iowa, USA.

Molecular Therapy. Nucleic Acids
|January 30, 2017
PubMed
Summary

This study presents a user-friendly, web-based bioinformatics approach for analyzing high-throughput sequencing data from aptamer selection processes. The method simplifies the identification and characterization of DNA and RNA aptamers for diagnostics and therapeutics.

Keywords:
SELEXaptamerhigh-throughput sequencingnext-generation sequencing

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Area of Science:

  • Biotechnology
  • Bioinformatics
  • Molecular Biology

Background:

  • Aptamers, selected via Systematic Evolution of Ligands by EXponential enrichment (SELEX), are crucial for diagnostics and therapeutics.
  • High-throughput sequencing (HTS) generates massive aptamer datasets, demanding advanced bioinformatics analysis.
  • Existing SELEX analysis methods can be complex and require significant computational resources.

Purpose of the Study:

  • To develop a semiautomated, accessible bioinformatics workflow for analyzing aptamer HTS data.
  • To leverage the Galaxy Project's web-based platform for SELEX data processing.
  • To facilitate the efficient identification and characterization of aptamer sequences.

Main Methods:

  • Utilized the Galaxy Project, a web-based bioinformatics platform, to create automated Workflows.
  • Processed large aptamer HTS datasets to compile databases of unique aptamer sequences.
  • Developed Workflows for analyzing aptamer abundance, persistence, and filtering.

Main Results:

  • Demonstrated efficient processing of aptamer HTS data using Galaxy Workflows.
  • Successfully compiled databases of unique aptamer sequences.
  • Enabled characterization and filtering of aptamer sequences based on abundance and persistence.

Conclusions:

  • The Galaxy-based approach offers a user-friendly, semiautomated solution for aptamer HTS data analysis.
  • This method simplifies aptamer discovery and characterization, accelerating development for diagnostic and therapeutic applications.
  • The web-based nature eliminates the need for extensive coding or software installation, democratizing HTS data analysis.