AptaGUI—A Graphical User Interface for the Efficient Analysis of HT-SELEX Data

To the Editor: Revolutionizing the traditional Systematic Evolution of Ligands by EXponential Enrichment (SELEX), high-throughput SELEX (HT-SELEX) has become the method of choice for the identification of aptamers—synthetic, single-stranded (ribo)nucleic molecules that bind to a given molecular target. 1 In contrast to traditional SELEX, in which only data from the last selection cycle is obtained, HT-SELEX allows for sequencing of every round (including control cycles) which are then jointly analyzed and interpreted. However, given the vast amount of data generated by this technology, purely text-based tools to visualize and manipulate aptamers have proven impractical and time consuming for many researchers in this field. Currently, COMPAS 2 by AptaIT is the only pipeline known to us to provide graphical navigation of HT-SELEX data but is licensed as proprietary software and only obtainable in conjunction with the purchase of an in vitro selection from the same company. We report AptaGUI, a new open-source and platform-independent graphical user interface (GUI) for the dynamic visualization of HT-SELEX data. In particular, AptaGUI includes support for applications of our AptaTools package that contains many useful algorithms for HT-SELEX analysis, including but not limited to data pre-processing, tracking the changes of individual aptamers, as well as entire aptamer family (groups of aptamers sharing highly similar nucleotide sequences), throughout selection cycles. This includes computing cycle-to-cycle enrichment of aptamers and their families and displaying them according to the user's specification. AptaGUI provides researchers with intuitive multi-scale access to any desired aspect of a SELEX experiment, ranging from general statistics such as quality control measures, nucleotide distributions, and diversity analysis of the individual rounds, through the intermediate representation of aptamer families as sequence logos, to detailed information on individual aptamers and their properties. It thus allows for capturing potential issues with the selection protocol, identification of candidate aptamers, and their detailed sequence and structure-based analysis among others. AptaGUI currently features four main sections focusing on (i) data quality control, (ii) experimental details such as enrichment statistics throughout selection cycles, (iii) sequence-based analysis, and (iv) aptamer family (cluster)–based analysis. In addition, AptaGUI provides secure, global, multiuser access to the data sets, hence enabling real-time, col-laborative studies in the field of aptamer discovery. AptaGUI is written in Java version 8 and uses a MySQL database containing all results produced by our software package AptaTools. AptaTools includes, in addition to basic analysis tools, the clustering algorithm AptaCLUSTER and the mutant analysis utility AptaMut. …