Efficient Pangenome Construction through Alignment-Free Residue Pangenome Analysis (ARPA)

Lal, A.; Moustafa, A. M.; Planet, P.

doi:10.1101/2022.06.03.494761

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bioRxiv · 10.1101/2022.06.03.494761

Efficient Pangenome Construction through Alignment-Free Residue Pangenome Analysis (ARPA)

Lal, A.·Moustafa, A. M.·Planet, P.

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Abstract

Protein sequences can be transformed into vectors composed of counts for each amino acid (vector of Residue Counts; vRC) that are mathematically tractable and retain information about homology. We use vRCs to perform alignment-free, residue-based, pangenome analysis (ARPA; https://github.com/Arnavlal/ARPA). ARPA is 70-90 times faster at identifying homologous gene clusters compared to standard techniques, and offers rapid calculation, visualization, and novel phylogenetic approaches for pangenomes.

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Lal, A., Moustafa, A. M., Planet, P.. 2022-06-05. Efficient Pangenome Construction through Alignment-Free Residue Pangenome Analysis (ARPA). https://doi.org/10.1101/2022.06.03.494761

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