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An Analysis of Symmetric Words in Human DNA: Adjacent vs Non-adjacent Word Distances

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Practical Applications of Computational Biology and Bioinformatics, 12th International Conference (PACBB2018 2018)

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 803))

Abstract

It is important to develop methods for finding DNA sites with high potential for the formation of hairpin/cruciform structures. In a previous work, we studied the distances between adjacent reversed complement words (symmetric words), and we observed that for some words some distances were favored. In the work presented here, we extended the study to the distance between non-adjacent reversed complement words and we observed strong periodicity in the distance distribution of some words. This may be an indication of potential for the formation of hairpin/cruciform structures.

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References

  1. Afreixo, V., Bastos, C.A.C., Pinho, A.J., Garcia, S.P., Ferreira, P.J.S.G.: Genome analysis with inter-nucleotide distances. Bioinformatics 25(23), 3064–3070 (2009)

    Google Scholar 

  2. Bastos, C.A.C., Afreixo, V., Garcia, S.P., Pinho, A.J.: Inter-stop symbol distances for the identification of coding regions. J. Integr. Bioinform. 10(3), 31–39 (2013)

    Google Scholar 

  3. Benson, G.: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27(2), 573 (1999)

    Article  Google Scholar 

  4. Bernard, G., Chan, C.X., Chan, Y.-B., Chua, X.-Y., Cong, Y., Hogan, J.M., Maetschke, S.R., Ragan, M.A.: Alignment-free inference of hierarchical and reticulate phylogenomic relationships. Brief. Bioinform., bbx067 (2017). https://doi.org/10.1093/bib/bbx067

  5. Cer, R.Z., Bruce, K.H., Mudunuri, U.S., Yi, M., Volfovsky, N., Luke, B.T., Bacolla, A., Collins, J.R., Stephens, R.M.: Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes. Nucleic Acids Res. 39(suppl. 1), D383–D391 (2010)

    Google Scholar 

  6. Hackenberg, M., Previti, C., Luque-Escamilla, P.L., Carpena, P., Martínez-Aroza, J., Oliver, J.L.: CpGcluster: a distance-based algorithm for CpG-island detection. BMC Bioinform. 7(1), 446 (2006)

    Google Scholar 

  7. Kolb, J., Chuzhanova, N.A., Högel, J., Vasquez, K.M., Cooper, D.N., Bacolla, A., Kehrer-Sawatzki, H.: Cruciform-forming inverted repeats appear to have mediated many of the microinversions that distinguish the human and chimpanzee genomes. Chromosome Res. 17(4), 469–483 (2009)

    Google Scholar 

  8. Sims, G.E., Kim, S.-H.: Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Proc. Nat. Acad. Sci. 108(20), 8329–8334 (2011)

    Article  Google Scholar 

  9. Smit, A.F.A., Hubley, R., Green, P.: Repeatmasker (1996)

    Google Scholar 

  10. Tavares, A.H.M.P., Pinho, A.J., Silva, R.M., Rodrigues, J.M.O.S., Bastos, C.A.C., Ferreira, P.J.S.G., Afreixo, V.: DNA word analysis based on the distribution of the distances between symmetric words. Sci. Rep. 7(1), 728 (2017)

    Article  Google Scholar 

  11. Wang, Y., Leung, F.C.C.: Long inverted repeats in eukaryotic genomes: recombinogenic motifs determine genomic plasticity. FEBS Lett. 580(5), 1277–1284 (2006)

    Article  Google Scholar 

Download references

Acknowledgment

This work was supported by FEDER (“Programa Operacional Fatores de Competitividade” COMPETE) and FCT (“Fundação para a Ciência e a Tecnologia”), within the projects UID/MAT/04106/2013 to CIDMA (Center for Research and Development in Mathematics and Applications) and UID/CEC/00127/2013 to IEETA (Institute of Electronics and Informatics Engineering of Aveiro).

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Authors and Affiliations

  1. IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Aveiro, Portugal

    Carlos A. C. Bastos, Vera Afreixo, João M. O. S. Rodrigues & Armando J. Pinho

  2. Department of Electronics, Telecommunications and Informatics, University of Aveiro, Aveiro, Portugal

    Carlos A. C. Bastos, João M. O. S. Rodrigues & Armando J. Pinho

  3. CIDMA-Center for Research and Development in Mathematics and Applications, Aveiro, Portugal

    Vera Afreixo

  4. Department of Mathematics, University of Aveiro, Aveiro, Portugal

    Vera Afreixo

Authors
  1. Carlos A. C. Bastos
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  2. Vera Afreixo
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  3. João M. O. S. Rodrigues
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  4. Armando J. Pinho
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Corresponding author

Correspondence to Carlos A. C. Bastos .

Editor information

Editors and Affiliations

  1. Escuela Superior de Ingeniería Informática, Universidad de Vigo, Ourense, Spain

    Florentino Fdez-Riverola

  2. Faculty of Computing, Department of Software Engineering, Universiti Teknologi Malaysia, Johor, Malaysia

    Mohd Saberi Mohamad

  3. Department de Informática, Universidade do Minho, Braga, Portugal

    Miguel Rocha

  4. Departamento de Informática y Automática, Facultad de Ciencias, Universidad de Salamanca, Salamanca, Spain

    Juan F. De Paz

  5. Departamento de Sistemas Informáticos, Universidad de Castilla-La Mancha, Albacete, Albacete, Spain

    Pascual González

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Bastos, C.A.C., Afreixo, V., Rodrigues, J.M.O.S., Pinho, A.J. (2019). An Analysis of Symmetric Words in Human DNA: Adjacent vs Non-adjacent Word Distances. In: Fdez-Riverola, F., Mohamad, M., Rocha, M., De Paz, J., González, P. (eds) Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. PACBB2018 2018. Advances in Intelligent Systems and Computing, vol 803. Springer, Cham. https://doi.org/10.1007/978-3-319-98702-6_10

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