Pangenome comparison via ED strings
As for efficiency, we compare the runtime of the intersection graph method against the classic product automaton construction showing that the intersection graph is faster by up to one order of magnitude. For showing effectiveness, we used real SARS-CoV-2 datasets and our matching statistics similarity measure to reproduce a well-established clade classification of SARS-CoV-2, thus demonstrating that the classification obtained by our method is in accordance with the existing one.
Authors
- Michelle Sweering (ORCID: https://orcid.org/0000-0003-1200-6015)
- Solon P. Pissis (ORCID: https://orcid.org/0000-0002-1445-1932)
- Estéban Gabory (ORCID: https://orcid.org/0000-0002-9897-1512)
- Moses Njagi Mwaniki (ORCID: https://orcid.org/0000-0002-4858-2375)
- Nadia Pisanti (ORCID: https://orcid.org/0000-0003-3915-7665)
- Jakub Radoszewski (ORCID: https://orcid.org/0000-0002-0067-6401)
- Wiktor Zuba (ORCID: https://orcid.org/0000-0002-1988-3507)
Institutions
- University of Pisa (IT)
- Centrum Wiskunde & Informatica (NL)
- University of Warsaw (PL)
- Vrije Universiteit Amsterdam (NL)
Publication Details
- Journal
- Frontiers in Bioinformatics
- Published
- 2024-09-26
- DOI
- https://doi.org/10.3389/fbinf.2024.1397036
- Citations
- 5
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 1.17
Funders
- Horizon 2020