Unbiased anchors for reliable genome-wide synteny detection

dc.contributor.authorKäther, Karl K.
dc.contributor.authorRemmel, Andreas
dc.contributor.authorLemke, Steffen
dc.contributor.authorStadler, Peter F.
dc.contributor.corporateKäther, Karl K.; Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstrasse 16-18, D-04017, Leipzig, Germany
dc.contributor.corporateRemmel, Andreas; Zoology Department, University of Hohenheim, 10587, Stuttgart, Germany
dc.contributor.corporateLemke, Steffen; Zoology Department, University of Hohenheim, 10587, Stuttgart, Germany
dc.contributor.corporateStadler, Peter F.; Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstrasse 16-18, D-04017, Leipzig, Germany
dc.date.accessioned2025-07-07T12:06:18Z
dc.date.available2025-07-07T12:06:18Z
dc.date.issued2025
dc.date.updated2025-07-03T13:03:47Z
dc.description.abstractOrthology 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.en
dc.description.sponsorshipOpen Access funding enabled and organized by Projekt DEAL.
dc.description.sponsorshipDFG
dc.description.sponsorshipUniversität Leipzig (1039)
dc.identifier.urihttps://doi.org/10.1186/s13015-025-00275-9
dc.identifier.urihttps://hohpublica.uni-hohenheim.de/handle/123456789/17915
dc.language.isoeng
dc.rights.licensecc_by
dc.subjectSynteny
dc.subjectAnchor
dc.subjectK-mer
dc.subject.ddc570
dc.titleUnbiased anchors for reliable genome-wide synteny detectionen
dc.type.diniArticle
dcterms.bibliographicCitationAlgorithms for molecular biology, 20 (2025), 5. https://doi.org/10.1186/s13015-025-00275-9. ISSN: 1748-7188 London : BioMed Central
dcterms.bibliographicCitation.articlenumber5
dcterms.bibliographicCitation.issn1748-7188
dcterms.bibliographicCitation.journaltitleAlgorithms for molecular biology
dcterms.bibliographicCitation.originalpublishernameBioMed Central
dcterms.bibliographicCitation.originalpublisherplaceLondon
dcterms.bibliographicCitation.volume20
local.export.bibtex@article{Käther2025, doi = {10.1186/s13015-025-00275-9}, author = {Käther, Karl K. and Remmel, Andreas and Lemke, Steffen et al.}, title = {Unbiased anchors for reliable genome-wide synteny detection}, journal = {Algorithms for Molecular Biology}, year = {2025}, volume = {20}, number = {1}, }
local.export.bibtexAuthorKäther, Karl K. and Remmel, Andreas and Lemke, Steffen et al.
local.export.bibtexKeyKäther2025
local.export.bibtexType@article
local.title.fullUnbiased anchors for reliable genome-wide synteny detection

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