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In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

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Published on: September 7, 2022

AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected

Dario Ruiz-Ciancio^1,2,3, Suresh Veeramani^4,5, Rahul Singh⁶

¹Instituto de Ciencias Biomédicas (ICBM), Facultad de Ciencias Médicas, Universidad Católica de Cuyo, Av. José Ignacio de la Roza 1516, Rivadavia 5400, San Juan, Argentina.

Molecular Therapy. Nucleic Acids

|November 7, 2024

Summary

AptamerRunner is a new algorithm that analyzes next-generation sequencing data to identify promising aptamers. It integrates computation and visualization to improve the selection of validated aptamers.

Keywords:

AptamerRunner Cytoscape MT: Bioinformatics aptamer bioinformatics clustering edit distance sequence analysis structure analysis tree distance

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Last Updated: Jun 8, 2025

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

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Published on: September 7, 2022

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Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

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Published on: January 7, 2017

Area of Science:

Biotechnology
Bioinformatics
Molecular Biology

Background:

Aptamers are DNA/RNA molecules with high target affinity, selected via SELEX.
Next-generation sequencing (NGS) enhances aptamer analysis compared to Sanger sequencing.
Identifying optimal aptamer candidates from NGS data remains a challenge.

Purpose of the Study:

To present AptamerRunner, a novel algorithm for aptamer sequence and structure clustering.
To integrate computational analysis with visualization for improved aptamer selection.
To facilitate the identification of high-likelihood candidate aptamers for experimental validation.

Main Methods:

Developed AptamerRunner, a clustering algorithm for aptamer NGS datasets.
Integrated computational analysis with visualization tools.
Incorporated expertise-directed decision-making into the workflow.

Main Results:

AptamerRunner provides a visual context for networked aptamers and ranking data.
The algorithm facilitates the selection of candidate aptamers based on fold enrichment and scoring.
Offers a significant advancement over existing aptamer clustering tools.

Conclusions:

AptamerRunner enhances the identification of validated aptamers from NGS data.
The tool's flexibility and user-friendly design benefit aptamer researchers.
Future enhancements promise broader applications across disciplines.