Abstract
The Adjacency Graph is a structure used to model genomes in several rearrangement distance problems. In particular, most studies use properties of a maximum cycle packing of this graph to develop bounds and algorithms for rearrangement distance problems, such as the reversal distance and the Double Cut and Join (DCJ) distance. When each genome has no repeated genes, there exists only one cycle packing for the graph. However, when each genome may have repeated genes, the problem of finding a maximum cycle packing for the adjacency graph (Adjacency Graph Packing) is NP-hard. In this work, we developed a greedy random heuristic and a genetic algorithm heuristic for the Adjacency Graph Packing problem for genomes with repeated genes. We present experimental results and compare these heuristics with the SOAR framework. Furthermore, we show how the solutions from our algorithms can improve the estimation for the reversal distance when compared to the SOAR framework. Lastly, we applied our genetic algorithm heuristic in real genomic data to validate its practical use.
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Notes
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Illustration created using treeio R package [14].
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Acknowledgments
This work was supported by the National Council of Technological and Scientific Development, CNPq (grant 425340/2016-3), the Coordenação de Aperfeiçoamento de Pessoal de NÃvel Superior - Brasil (CAPES) - Finance Code 001, and the São Paulo Research Foundation, FAPESP (grants 2013/08293-7, 2015/11937-9, 2017/12646-3, and 2019/27331-3).
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Siqueira, G., Oliveira, A.R., Alexandrino, A.O., Dias, Z. (2021). Heuristics for Cycle Packing of Adjacency Graphs for Genomes with Repeated Genes. In: Stadler, P.F., Walter, M.E.M.T., Hernandez-Rosales, M., Brigido, M.M. (eds) Advances in Bioinformatics and Computational Biology. BSB 2021. Lecture Notes in Computer Science(), vol 13063. Springer, Cham. https://doi.org/10.1007/978-3-030-91814-9_9
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