PymiRa: A rapid and accurate classification tool for small non-coding RNAs, including microRNAs

Small non-coding RNAs (sncRNA; < 200 nucleotide length) are of increasing research interest due to their key regulatory roles in a host of fundamental biological processes. For example, microRNAs (miRNAs), a specific class of sncRNAs, regulate gene expression through messenger RNA (mRNA) interactions, and their dysregulation is associated with disease. Classifying sncRNAs is an important bioinformatic task in small RNA-sequencing pipelines. Here we have developed an aligner called PymiRa, written in Python, to identify and quantify miRNAs from FASTA/FASTQ sequencing files. Unlike other approaches, PymiRa utilises a Burrows-Wheeler algorithm to align an input file against a reference hairpin precursor FASTA file derived from miRBase, the online miRNA registry, permitting up to two mismatches at the 3' end of a read. Previous tools used either a Burrows-Wheeler genome alignment or dynamic programming alignment to precursors; we demonstrate that combining both approaches yields improved results and efficiency. Importantly, the PymiRa aligner accounts for 3' post-transcriptional modifications to miRNAs that typically occur. PymiRa is a fast, accurate, and publicly accessible aligner available via GitHub and/or a webserver for sncRNA identification, including miRNAs, enabling accurate counts to be produced as part of a small RNA-sequencing pipeline. PymiRa will undergo relevant revisions over time e.g., with miRBase version updates. The PymiRa aligner will facilitate a deeper biological understanding of the landscape of sncRNA expression in normal physiological conditions and their dysregulation in disease states, including cancer.