Abstract
The improvements in DNA sequence technologies have increased the volume and speed at which genomic data is acquired. Nevertheless, due to the difficulties for completely assembling 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 genomes by comparing extracted paths from de Bruijn graphs and comparing such paths. The idea of using data from de Bruijn graphs is interesting because such graphs are built by many practical genome assemblers. In this article we introduce gcBB, a method for comparing genomes represented as succinct de Bruijn graphs directly, without resorting to sequence alignments, by means of the entropy and expectation measures based on the Burrows-Wheeler Similarity Distribution (BWSD). We have compared phylogenies of genomes obtained by other methods to those obtained with gcBB, achieving promising results.
Keywords
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Acknowledgements
The authors thank Prof. Marinella Sciortino for helpful discussions and thank Prof. Nalvo Almeida for granting access to the computer used in the experiments.
Funding
L.P.R. acknowledges that this study was financed by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brazil, Financing Code 001. F.A.L. acknowledges the financial support from CNPq (grant number 406418/2021-7) and FAPEMIG (grant number APQ-01217-22). G.P.T. acknowledges the financial support of Brazilian agencies CNPq and CAPES.
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Ramos, L.P., Louza, F.A., Telles, G.P. (2022). Genome Comparison on Succinct Colored de Bruijn Graphs. In: Arroyuelo, D., Poblete, B. (eds) String Processing and Information Retrieval. SPIRE 2022. Lecture Notes in Computer Science, vol 13617. Springer, Cham. https://doi.org/10.1007/978-3-031-20643-6_12
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