Fast characterization of segmental duplication structure in multiple genome assemblies

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buir.contributor.authorAlkan, Can
buir.contributor.orcidAlkan, Can|0000-0002-5443-0706
dc.citation.epage15en_US
dc.citation.issueNumber1en_US
dc.citation.spage1en_US
dc.citation.volumeNumber17en_US
dc.contributor.authorIšerić, Hamza
dc.contributor.authorAlkan, Can
dc.contributor.authorHach, Faraz
dc.contributor.authorNumanagić, Ibrahim
dc.date.accessioned2023-03-01T08:19:03Z
dc.date.available2023-03-01T08:19:03Z
dc.date.issued2022-12
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractMotivation: The increasing availability of high-quality genome assemblies raised interest in the characterization of genomic architecture. Major architectural elements, such as common repeats and segmental duplications (SDs), increase genome plasticity that stimulates further evolution by changing the genomic structure and inventing new genes. Optimal computation of SDs within a genome requires quadratic-time local alignment algorithms that are impractical due to the size of most genomes. Additionally, to perform evolutionary analysis, one needs to characterize SDs in multiple genomes and find relations between those SDs and unique (non-duplicated) segments in other genomes. A naïve approach consisting of multiple sequence alignment would make the optimal solution to this problem even more impractical. Thus there is a need for fast and accurate algorithms to characterize SD structure in multiple genome assemblies to better understand the evolutionary forces that shaped the genomes of today. Results: Here we introduce a new approach, BISER, to quickly detect SDs in multiple genomes and identify elementary SDs and core duplicons that drive the formation of such SDs. BISER improves earlier tools by (i) scaling the detection of SDs with low homology to multiple genomes while introducing further 7–33× speed-ups over the existing tools, and by (ii) characterizing elementary SDs and detecting core duplicons to help trace the evolutionary history of duplications to as far as 300 million years. Availability and implementation: BISER is implemented in Seq programming language and is publicly available at https://github.com/0xTCG/biser. © 2022, The Author(s).en_US
dc.identifier.doi10.1186/s13015-022-00210-2en_US
dc.identifier.issn17487188
dc.identifier.urihttp://hdl.handle.net/11693/111987
dc.language.isoEnglishen_US
dc.publisherBioMed Central Ltden_US
dc.relation.isversionofhttps://dx.doi.org/10.1186/s13015-022-00210-2en_US
dc.source.titleAlgorithms for Molecular Biologyen_US
dc.subjectFast alignmenten_US
dc.subjectGenome analysisen_US
dc.subjectSegmental duplicationsen_US
dc.subjectSequence decompositionen_US
dc.titleFast characterization of segmental duplication structure in multiple genome assembliesen_US
dc.typeArticleen_US

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