BISER: 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.epage15:18en_US
dc.citation.spage15:1en_US
dc.citation.volumeNumber201en_US
dc.contributor.authorIšerić, Hamza
dc.contributor.authorAlkan, Can
dc.contributor.authorHach, Faraz
dc.contributor.authorNumanagić, Ibrahim
dc.contributor.editorCarbone, Alessandra
dc.contributor.editorEl-Kebir, Mohammed
dc.coverage.spatialDagstuhl, Germanyen_US
dc.date.accessioned2022-02-04T08:18:40Z
dc.date.available2022-02-04T08:18:40Z
dc.date.issued2021-07-22
dc.departmentDepartment of Computer Engineeringen_US
dc.descriptionConference Name: 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)en_US
dc.descriptionDate of Conference: 2021en_US
dc.description.abstractThe increasing availability of high-quality genome assemblies raised interest in the characterization of genomic architecture. Major architectural parts, such as common repeats and segmental duplications (SDs), increase genome plasticity that stimulates further evolution by changing the genomic structure. However, optimal computation of SDs through standard local alignment algorithms is impractical due to the size of most genomes. A cross-genome evolutionary analysis of SDs is even harder, as one needs to characterize SDs in multiple genomes and find relations between those SDs and unique segments in other genomes. 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. Here we introduce a new tool, 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 (75%) to multiple genomes while introducing further 8-24x 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 90 million years.en_US
dc.identifier.doi10.4230/LIPIcs.WABI.2021.15en_US
dc.identifier.isbn978-3-95977-200-6
dc.identifier.issn1868-8969
dc.identifier.urihttp://hdl.handle.net/11693/77035
dc.language.isoEnglishen_US
dc.publisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatiken_US
dc.relation.isversionofhttps://dx.doi.org/10.4230/LIPIcs.WABI.2021.15en_US
dc.source.titleLeibniz International Proceedings in Informatics, LIPIcen_US
dc.subjectGenome analysisen_US
dc.subjectFast alignmenten_US
dc.subjectSegmental duplicationsen_US
dc.subjectCore dupliconsen_US
dc.subjectSequence decompositionen_US
dc.titleBISER: fast characterization of segmental duplication structure in multiple genome assembliesen_US
dc.typeConference Paperen_US

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