Abstract
In this paper, we propose a computational approach to quantify inverted repeats. This is important, because it is known that the presence of inverted repeats in genomic data may be associated to certain chromosomal rearrangements. First, we present a reference-based relative compression method, which employs statistical characteristics of the genomic data. Then, for determining the similarity between genomic sequences, we use the normalized relative compression measure, which is light-weight regarding computational time and memory. Testing this approach on various species, including human, chimpanzee, gorilla, chicken, turkey and archaea genomes, we unveil unreported results that may support several evolution insights.
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Acknowledgments
We would like to thank the FCT—Foundation for Science and Technology in Portugal, for their support of this research, within the Doctoral Programme FCT MAP-i in Computer Science, and also acknowledge european funds through FEDER, under the COMPETE 2020 and Portugal 2020 programs, in the context of the projects UID/CEC/00127/2013 and PTDC/EEI-SII/6608/2014.
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Hosseini, M., Pratas, D., Pinho, A.J. (2017). On the Role of Inverted Repeats in DNA Sequence Similarity. In: Fdez-Riverola, F., Mohamad, M., Rocha, M., De Paz, J., Pinto, T. (eds) 11th International Conference on Practical Applications of Computational Biology & Bioinformatics. PACBB 2017. Advances in Intelligent Systems and Computing, vol 616. Springer, Cham. https://doi.org/10.1007/978-3-319-60816-7_28
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DOI: https://doi.org/10.1007/978-3-319-60816-7_28
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