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| Main Authors: | , , |
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| Format: | Preprint |
| Published: |
2024
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2411.09114 |
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| _version_ | 1866929591014129664 |
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| author | Ramos, Lucas P. Louza, Felipe A. Telles, Guilherme P. |
| author_facet | Ramos, Lucas P. Louza, Felipe A. Telles, Guilherme P. |
| contents | DNA technologies have evolved significantly in the past years enabling the sequencing of a large number of genomes in a short time. Nevertheless, the underlying computational problem is hard, and many technical factors and limitations complicate obtaining the complete sequence of a genome. Many genomes are left in a draft state, in which each chromosome is represented by a set of sequences with partial information on their relative order. Recently, some approaches have been proposed to compare draft genomes by comparing paths in de Bruijn graphs, which are constructed by many practical genome assemblers. In this article we introduce gcBB, a method for comparing genomes represented as succinct colored de Bruijn graphs directly, without resorting to sequence alignments, by means of the entropy and expectation measures based on the Burrows-Wheeler Similarity Distribution. We also introduce an improved version of gcBB, called mgcBB, that improves the time performance considerably through the selection of different data structures. We have compared phylogenies of genomes obtained by other methods to those obtained with gcBB, achieving promising results. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2411_09114 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Comparative genomics with succinct colored de Bruijn graphs Ramos, Lucas P. Louza, Felipe A. Telles, Guilherme P. Data Structures and Algorithms DNA technologies have evolved significantly in the past years enabling the sequencing of a large number of genomes in a short time. Nevertheless, the underlying computational problem is hard, and many technical factors and limitations complicate obtaining the complete sequence of a genome. Many genomes are left in a draft state, in which each chromosome is represented by a set of sequences with partial information on their relative order. Recently, some approaches have been proposed to compare draft genomes by comparing paths in de Bruijn graphs, which are constructed by many practical genome assemblers. In this article we introduce gcBB, a method for comparing genomes represented as succinct colored de Bruijn graphs directly, without resorting to sequence alignments, by means of the entropy and expectation measures based on the Burrows-Wheeler Similarity Distribution. We also introduce an improved version of gcBB, called mgcBB, that improves the time performance considerably through the selection of different data structures. We have compared phylogenies of genomes obtained by other methods to those obtained with gcBB, achieving promising results. |
| title | Comparative genomics with succinct colored de Bruijn graphs |
| topic | Data Structures and Algorithms |
| url | https://arxiv.org/abs/2411.09114 |