BWT for string collections
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arXiv
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| Main Authors: | , , , , |
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| Format: | Preprint |
| Published: |
2025
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| _version_ | 1866915317725265920 |
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| author | Cenzato, Davide Lipták, Zsuzsanna Pisanti, Nadia Rosone, Giovanna Sciortino, Marinella |
| author_facet | Cenzato, Davide Lipták, Zsuzsanna Pisanti, Nadia Rosone, Giovanna Sciortino, Marinella |
| contents | We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipták, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT variants and give a categorization of publicly available tools for computing the BWT of string collections. We show how the specific method used impacts on the resulting transform, including the number of runs, and on the dynamicity of the transform with respect to adding or removing strings from the collection. We then focus on the number of runs of these BWT variants and present the optimal BWT introduced in [Cenzato et al., DCC 2023], which implements an algorithm originally proposed by [Bentley et al., ESA 2020] to minimize the number of BWT-runs. We also discuss several recent heuristics and study their impact on the compression of biological sequences. We conclude with an overview of the applications and the impact of the BWT of string collections in bioinformatics. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2506_01092 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | BWT for string collections Cenzato, Davide Lipták, Zsuzsanna Pisanti, Nadia Rosone, Giovanna Sciortino, Marinella Data Structures and Algorithms We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipták, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT variants and give a categorization of publicly available tools for computing the BWT of string collections. We show how the specific method used impacts on the resulting transform, including the number of runs, and on the dynamicity of the transform with respect to adding or removing strings from the collection. We then focus on the number of runs of these BWT variants and present the optimal BWT introduced in [Cenzato et al., DCC 2023], which implements an algorithm originally proposed by [Bentley et al., ESA 2020] to minimize the number of BWT-runs. We also discuss several recent heuristics and study their impact on the compression of biological sequences. We conclude with an overview of the applications and the impact of the BWT of string collections in bioinformatics. |
| title | BWT for string collections |
| topic | Data Structures and Algorithms |
| url | https://arxiv.org/abs/2506.01092 |