Unbiased anchors for reliable genome-wide synteny detection
Abstract 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 orde...
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| Format: | Article |
| Language: | English |
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BMC
2025-04-01
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| Series: | Algorithms for Molecular Biology |
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| Online Access: | https://doi.org/10.1186/s13015-025-00275-9 |
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| author | Karl K. Käther Andreas Remmel Steffen Lemke Peter F. Stadler |
| author_facet | Karl K. Käther Andreas Remmel Steffen Lemke Peter F. Stadler |
| author_sort | Karl K. Käther |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-b0d2ae76dff141ef8d799fdba1211379 |
| institution | OA Journals |
| issn | 1748-7188 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj-art-b0d2ae76dff141ef8d799fdba12113792025-08-20T02:25:34ZengBMCAlgorithms for Molecular Biology1748-71882025-04-0120111210.1186/s13015-025-00275-9Unbiased anchors for reliable genome-wide synteny detectionKarl K. Käther0Andreas Remmel1Steffen Lemke2Peter F. Stadler3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig UniversityZoology Department, University of HohenheimZoology Department, University of HohenheimBioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig UniversityAbstract 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.https://doi.org/10.1186/s13015-025-00275-9SyntenyAnchork-mer |
| spellingShingle | Karl K. Käther Andreas Remmel Steffen Lemke Peter F. Stadler Unbiased anchors for reliable genome-wide synteny detection Algorithms for Molecular Biology Synteny Anchor k-mer |
| title | Unbiased anchors for reliable genome-wide synteny detection |
| title_full | Unbiased anchors for reliable genome-wide synteny detection |
| title_fullStr | Unbiased anchors for reliable genome-wide synteny detection |
| title_full_unstemmed | Unbiased anchors for reliable genome-wide synteny detection |
| title_short | Unbiased anchors for reliable genome-wide synteny detection |
| title_sort | unbiased anchors for reliable genome wide synteny detection |
| topic | Synteny Anchor k-mer |
| url | https://doi.org/10.1186/s13015-025-00275-9 |
| work_keys_str_mv | AT karlkkather unbiasedanchorsforreliablegenomewidesyntenydetection AT andreasremmel unbiasedanchorsforreliablegenomewidesyntenydetection AT steffenlemke unbiasedanchorsforreliablegenomewidesyntenydetection AT peterfstadler unbiasedanchorsforreliablegenomewidesyntenydetection |