Graphite: painting genomes using a colored de Bruijn graph.
| Autor: | Beeloo R; Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands., Zomer AL; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, The Netherlands., Deorowicz S; Department of Algorithmics and Software, Silesian University of Technology, Akademicka 16, Gliwice PL-44100, Poland., Dutilh BE; Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.; Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany. |
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| Jazyk: | angličtina |
| Zdroj: | NAR genomics and bioinformatics [NAR Genom Bioinform] 2024 Oct 23; Vol. 6 (4), pp. lqae142. Date of Electronic Publication: 2024 Oct 23 (Print Publication: 2024). |
| DOI: | 10.1093/nargab/lqae142 |
| Abstrakt: | The recent growth of microbial sequence data allows comparisons at unprecedented scales, enabling the tracking of strains, mobile genetic elements, or genes. Querying a genome against a large reference database can easily yield thousands of matches that are tedious to interpret and pose computational challenges. We developed Graphite that uses a colored de Bruijn graph (cDBG) to paint query genomes, selecting the local best matches along the full query length. By focusing on the best genomic match of each query region, Graphite reduces the number of matches while providing the most promising leads for sequence tracking or genomic forensics. When applied to hundreds of Campylobacter genomes we found extensive gene sharing, including a previously undetected C. coli plasmid that matched a C. jejuni chromosome. Together, genome painting using cDBGs as enabled by Graphite, can reveal new biological phenomena by mitigating computational hurdles. (© The Author(s) 2024. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.) |
| Databáze: | MEDLINE |
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