BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies

Authors Hamza Išerić, Can Alkan, Faraz Hach, Ibrahim Numanagić

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Author Details

Hamza Išerić
  • Department of Computer Science, University of Victoria, Canada
Can Alkan
  • Department of Computer Engineering, Bilkent University, Ankara, Turkey
Faraz Hach
  • Vancouver Prostate Centre, Canada
Ibrahim Numanagić
  • Department of Computer Science, University of Victoria, Canada


We thank Haris Smajlović for his invaluable comments and suggestions during the manuscript preparation.

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Hamza Išerić, Can Alkan, Faraz Hach, and Ibrahim Numanagić. BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 15:1-15:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)


The 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.

Subject Classification

ACM Subject Classification
  • Applied computing → Bioinformatics
  • genome analysis
  • fast alignment
  • segmental duplications
  • core duplicons
  • sequence decomposition


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