The Bioinformatics of Aptamers: HT-SELEX Analysis with AptaSUITE.

Abstract

Next-generation systematic evolution of ligands by exponential enrichment approaches consistently combine the experimental protocol with high-throughput sequencing after each round of selection. This extension, known as HT-SELEX, results in a vast amount of raw sequencing data that requires tailored bioinformatics approaches to efficiently process and analyze these reads. Here, we present a step-by-step walkthrough of AptaSUITE, a previously published, open-source, and platform-independent software collection of peer-reviewed bioinformatics tools for HT-SELEX data, integrated into a convenient and efficient graphical user interface. We highlight AptaSUITE's main components and illustrate their utility for a variety of usage scenarios. These include, but are not limited to, computational solutions for data preprocessing such as demultiplexing and quality control, aptamer candidate identification, as well as binding motif elucidation. Taken together, AptaSUITE comprises a complete bioinformatics solution for HT-SELEX data analysis while providing real-time, intuitive, and graphical access to the aptamer information.