ricME: Long-Read Based Mobile Element Variant Detection Using Sequence Realignment and Identity Calculation

Huidong Ma, Cheng Zhong*, Hui Sun, Danyang Chen, HaiXiang Lin

*Corresponding author for this work

Research output: Chapter in Book/Conference proceedings/Edited volumeConference contributionScientificpeer-review

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Abstract

The mobile element variant is a very important structural variant, accounting for a quarter of structural variants, and it is closely related to many issues such as genetic diseases and species diversity. However, few detection algorithms of mobile element variants have been developed on third-generation sequencing data. We propose an algorithm ricME that combines sequence realignment and identity calculation for detecting mobile element variants. The ricME first performs an initial detection to obtain the positions of insertions and deletions, and extracts the variant sequences; then applies sequence realignment and identity calculation to obtain the transposon classes related to the variant sequences; finally, adopts a multi-level judgment rule to achieve accurate detection of mobile element variants based on the transposon classes and identities. Compared with a representative long-read based mobile element variant detection algorithm rMETL, the ricME improves the F1-score by 11.5 and 21.7% on simulated datasets and real datasets, respectively.

Original languageEnglish
Title of host publicationBioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings
EditorsXuan Guo, Serghei Mangul, Murray Patterson, Alexander Zelikovsky
Place of PublicationSingapore
PublisherSpringer
Pages165-177
Number of pages13
ISBN (Electronic)978-981-99-7074-2
ISBN (Print)978-981-99-7073-5
DOIs
Publication statusPublished - 2023
Event19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023 - Wroclaw, Poland
Duration: 9 Oct 202312 Oct 2023

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume14248 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023
Country/TerritoryPoland
CityWroclaw
Period9/10/2312/10/23

Bibliographical note

Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care
Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.

Keywords

  • identity calculation
  • mobile element variants
  • sequence realignment
  • third-generation sequencing data

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