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AptaPLEX - A dedicated, multithreaded demultiplexer for HT-SELEX data.

Jan Hoinka1, Teresa Przytycka1

  • 1National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA.

Methods (San Diego, Calif.)
|April 16, 2016
PubMed
Summary

AptaPLEX is a new software tool that demultiplexes high-throughput sequencing data from Systematic Evolution of Ligands by Exponential Enrichment (SELEX) experiments. It processes complex aptamer data, enabling more efficient analysis of these crucial molecules.

Keywords:
AptamersDemultiplexingHT-SELEXQuality control

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Area of Science:

  • Biotechnology
  • Bioinformatics
  • Molecular Biology

Background:

  • Aptamers are key molecules for diagnostics and therapeutics, identified through Systematic Evolution of Ligands by Exponential Enrichment (SELEX).
  • High-throughput sequencing (HT-SELEX) generates vast amounts of data requiring specialized preprocessing.
  • Current solutions for HT-SELEX data preprocessing are often integrated into larger pipelines, limiting standalone use.

Purpose of the Study:

  • To introduce AptaPLEX, a standalone, platform-independent demultiplexer for HT-SELEX data.
  • To provide a tool for efficient extraction and restoration of aptamers from multiplexed sequencing reads.
  • To facilitate in silico analysis of aptamer selection stages.

Main Methods:

  • AptaPLEX identifies and extracts aptamer sequences by recognizing barcode and primer regions within sequencing reads.
  • The software employs fuzzy matching for barcodes and primers, accommodating variations.
  • It automatically corrects mismatches in paired-end sequencing data.

Main Results:

  • Aptaplex successfully demultiplexes HT-SELEX data, restoring aptamers to their original selection cycles.
  • The software handles multiplexed data from multiple experiments.
  • It offers robust error correction for barcode and primer regions, including paired-end data.

Conclusions:

  • AptaPLEX is a versatile and user-friendly solution for HT-SELEX data preprocessing.
  • Its standalone nature and platform independence enhance its applicability across various computational environments.
  • The software simplifies and accelerates the analysis of aptamer selection processes.