Browsing by Subject "Synteny"

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Unbiased anchors for reliable genome-wide synteny detection
(2025) Käther, Karl K.; Remmel, Andreas; Lemke, Steffen; Stadler, Peter F.; Käther, Karl K.; Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstrasse 16-18, D-04017, Leipzig, Germany; Remmel, Andreas; Zoology Department, University of Hohenheim, 10587, Stuttgart, Germany; Lemke, Steffen; Zoology Department, University of Hohenheim, 10587, Stuttgart, Germany; Stadler, Peter F.; Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstrasse 16-18, D-04017, Leipzig, Germany
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.