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February 1st, 2025
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Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena
bioinformatics
biorxiv

AnchoRNA: Full virus genome alignments through conserved anchor regions

Eulenfeld, T.Open in Google Scholar•Triebel, S.Open in Google Scholar•Marz, M.Open in Google Scholar

Motivation: Multiple sequence alignment of full viral genomes can be challenging due to factors such as long sequences, large insertions/deletions (spanning several 100 nucleotides), high number of sequences, sequence divergence, and high computational complexity, as e.g., in the context of secondary structure prediction. Standard alignment methods often face these issues, especially when processing highly variable sequences or when specific phylogenetic analysis is required on selected subsequences. We present AnchoRNA, a Python-based command line tool designed to identify conserved regions, or anchors, within coding sequences. These anchors define split positions, guiding the alignment of complex viral genomes, including those with significant secondary structures. AnchoRNA enhances the accuracy and efficiency of full-genome alignment by focusing on these crucial conserved regions. The presented approach can be particularly useful when designing primers conserved across a virus family. Results: AnchoRNA guided alignments are systematically compared to the results of 3 alignment programs. Utilizing a dataset of 55 representative Pestivirus genomes, AnchoRNA identified 56 anchors that are crucial for guiding the alignment process. The incorporation of these anchors led to significant improvements across all tested alignment tools, highlighting the effectiveness of AnchoRNA in enhancing alignment quality, especially in complex viral genomes. Availability: AnchoRNA is available to the scientific community under the MIT license on GitHub at https://github.com/rnajena/anchorna, with releases archived on Zenodo. The package includes a tutorial featuring a Pestivirus dataset and is compatible with all platforms that support Python.

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