Tool and Algorithm for the Determination of Aptamers in Nanopore Sequencing Data: AptaLong

Abstract

Nanopore sequencing is a third generation sequencing technology that allows direct, real-time sequencing of individual DNA or RNA molecules. It utilizes a nanopore – an extremely small pore – in a membrane to pass a single strand DNA or RNA. As the sequence passes through the nanopore, changes in electrical current are detected and used to determine the nucleotide sequence. Nanopore sequencing has several advantages. It offers long read lengths, allowing for the sequencing of difficult regions of the genome, such as repetitive regions. It also enables real-time sequencing, providing immediate data generation without the need for extensive library preparation. Many bioinformatics pipelines and tools have been developed specifically for nanopore sequencing data analysis, addressing the unique characteristics and challenges of this technology, while dealing with non-standard long reads, derived from the ligation process of shorter oligonucleotides, might be challenging. In this research we present a new algorithm that extracts an aptamer sequence from the results of nanopore sequencing of several SELEX experiments with single-stranded DNA. The algorithm is based on statistical methods, based on known primer sequences and length of searching aptamer. We used step-by-step displacement of the reference sequence with positional alignment and calculated the positional frequencies of each nucleotide. As a result, the nucleotide frequencies obtained at each step are averaged, and thus, we find the sequence that is more likely to represent the aptamer.