Unbiased anchors for reliable genome-wide synteny detection
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| Názov: | Unbiased anchors for reliable genome-wide synteny detection |
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| Autori: | Käther, Karl K, Remmel, Andreas, Lemke, Steffen, Stadler, Peter F |
| Zdroj: | Algorithms Mol Biol Algorithms for Molecular Biology, Vol 20, Iss 1, Pp 1-12 (2025) |
| Informácie o vydavateľovi: | Springer Science and Business Media LLC, 2025. |
| Rok vydania: | 2025 |
| Predmety: | Anchor, 106005 Bioinformatik, QH301-705.5, Research, k-mer, Genetics, Biology (General), QH426-470, 106005 Bioinformatics, Synteny |
| Popis: | Orthology inference lies at the foundation of comparative genomics research. The correct identification of loci which descended from a common ancestral sequence is not only complicated by sequence divergence but also duplication and other genome rearrangements. The conservation of gene order, i.e. synteny, is used in conjunction with sequence similarity as an additional factor for orthology determination. Current approaches, however, rely on genome annotations and are therefore limited. Here we present an annotation-free approach and compare it to synteny analysis with annotations. We find that our approach works better in closely related genomes whereas there is a better performance with annotations for more distantly related genomes. Overall, the presented algorithm offers a useful alternative to annotation-based methods and can outperform them in many cases. |
| Druh dokumentu: | Article Other literature type |
| Jazyk: | English |
| ISSN: | 1748-7188 |
| DOI: | 10.1186/s13015-025-00275-9 |
| Prístupová URL adresa: | https://pubmed.ncbi.nlm.nih.gov/40188341 https://doaj.org/article/b0d2ae76dff141ef8d799fdba1211379 |
| Rights: | CC BY |
| Prístupové číslo: | edsair.doi.dedup.....692f2cfb6875b6545e0681fe75408c1c |
| Databáza: | OpenAIRE |
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Nájsť tento článok vo Web of Science | Abstrakt: | Orthology inference lies at the foundation of comparative genomics research. The correct identification of loci which descended from a common ancestral sequence is not only complicated by sequence divergence but also duplication and other genome rearrangements. The conservation of gene order, i.e. synteny, is used in conjunction with sequence similarity as an additional factor for orthology determination. Current approaches, however, rely on genome annotations and are therefore limited. Here we present an annotation-free approach and compare it to synteny analysis with annotations. We find that our approach works better in closely related genomes whereas there is a better performance with annotations for more distantly related genomes. Overall, the presented algorithm offers a useful alternative to annotation-based methods and can outperform them in many cases. |
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| ISSN: | 17487188 |
| DOI: | 10.1186/s13015-025-00275-9 |