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Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT

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Bioinformatics and Biomedical Engineering (IWBBIO 2023)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13919))

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Abstract

Computing maximal perfect blocks of a given panel of haplotypes is a crucial task for efficiently solving problems such as polyploid haplotype reconstruction and finding identical-by-descent segments shared among individuals of a population. Unfortunately, the presence of missing data in the haplotype panel limits the usefulness of the notion of perfect blocks.

We propose a novel algorithm for computing maximal blocks in a panel with missing data (represented as wildcards). The algorithm is based on the Positional Burrows-Wheeler Transform (PBWT) and has been implemented in the tool Wild-pBWT, available at https://github.com/AlgoLab/Wild-pBWT/. Experimental comparison showed that Wild-pBWT is 10–15 times faster than another state-of-the-art approach, while using a negligible amount of memory.

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References

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Acknowledgements

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 872539.

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Authors and Affiliations

  1. DISCo, University of Milano - Bicocca, viale Sarca 336, Milano, Italy

    Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi & Mattia Sgrò

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  1. Paola Bonizzoni
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  2. Gianluca Della Vedova
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  3. Yuri Pirola
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  4. Raffaella Rizzi
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  5. Mattia Sgrò
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Corresponding author

Correspondence to Paola Bonizzoni .

Editor information

Editors and Affiliations

  1. University of Granada, Granada, Spain

    Ignacio Rojas

  2. University of Granada, Granada, Spain

    Olga Valenzuela

  3. University of Granada, Granada, Spain

    Fernando Rojas Ruiz

  4. University of Granada, Granada, Spain

    Luis Javier Herrera

  5. University of Granada, Granada, Spain

    Francisco Ortuño

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Bonizzoni, P., Della Vedova, G., Pirola, Y., Rizzi, R., Sgrò, M. (2023). Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT. In: Rojas, I., Valenzuela, O., Rojas Ruiz, F., Herrera, L.J., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2023. Lecture Notes in Computer Science(), vol 13919. Springer, Cham. https://doi.org/10.1007/978-3-031-34953-9_5

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  • DOI: https://doi.org/10.1007/978-3-031-34953-9_5

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-34952-2

  • Online ISBN: 978-3-031-34953-9

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