Visualization of Similar Primer and Adapter Sequences in Assembled Archaeal Genomes

Abstract

Primer and adapter sequences are synthetic DNA or RNA oligonucleotides used in the process of amplification and sequencing. In theory, while similar primer sequences can be present on assembled genomes, adapter sequences should be trimmed (filtered) and, hence, absent from assembled genomes. However, given ambiguity problems, inefficient parameterization of trimming tools, and others, uncommonly they can be found in assembled genomes, on an exact or approximate state. In this paper, we investigate the occurrence of exact and approximate primer-adapter subsequences in assembled and, specifically, in the whole archaeal genomes of the NCBI database. We present a new method that combines data compression with custom signal processing operations, namely filtering and segmentation, to localize and visualize these regions given a defined similarity threshold. The program is freely available, under GPLv3 license, at https://github.com/pratas/maple.