Dissimilar symmetric word pairs in the human genome

Ana Helena Tavares; Jakob Raymaekers; Peter J. Rousseeuw; Raquel M. Silva; Carlos A.C. Bastos; Armando Pinho; Paula Brito; Vera Afreixo

doi:10.1007/978-3-319-60816-7_30

Dissimilar symmetric word pairs in the human genome

Ana Helena Tavares^*, Jakob Raymaekers, Peter J. Rousseeuw, Raquel M. Silva, Carlos A.C. Bastos, Armando Pinho, Paula Brito, Vera Afreixo

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Citation (Scopus)

Abstract

In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions. Since symmetric pairs with different patterns could point to evolutionary features, we search for the pairs with the most dissimilar behaviour. We focus our study on the complete human genome and its repeat-masked version.

Original language	English
Title of host publication	11th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2017
Editors	Miguel Rocha, Juan F. De Paz, Tiago Pinto, Florentino Fdez-Riverola, Mohd Saberi Mohamad
Publisher	Springer Verlag
Pages	248-256
Number of pages	9
ISBN (Print)	9783319608150
DOIs	https://doi.org/10.1007/978-3-319-60816-7_30
Publication status	Published - 2017
Externally published	Yes
Event	11th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2017 - Porto, Portugal Duration: 21 Jun 2017 → 23 Jun 2017

Publication series

Name	Advances in Intelligent Systems and Computing
Volume	616
ISSN (Print)	2194-5357

Conference

Conference	11th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2017
Country/Territory	Portugal
City	Porto
Period	21/06/17 → 23/06/17

Keywords

Dissimilarity measure
Human genome
Inter-word distance
Reversed complements

Access to Document

10.1007/978-3-319-60816-7_30

Cite this

Tavares, A. H., Raymaekers, J., Rousseeuw, P. J., Silva, R. M., Bastos, C. A. C., Pinho, A., Brito, P., & Afreixo, V. (2017). Dissimilar symmetric word pairs in the human genome. In M. Rocha, J. F. De Paz, T. Pinto, F. Fdez-Riverola, & M. S. Mohamad (Eds.), 11th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2017 (pp. 248-256). (Advances in Intelligent Systems and Computing; Vol. 616). Springer Verlag. https://doi.org/10.1007/978-3-319-60816-7_30

Tavares, Ana Helena ; Raymaekers, Jakob ; Rousseeuw, Peter J. et al. / Dissimilar symmetric word pairs in the human genome. 11th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2017. editor / Miguel Rocha ; Juan F. De Paz ; Tiago Pinto ; Florentino Fdez-Riverola ; Mohd Saberi Mohamad. Springer Verlag, 2017. pp. 248-256 (Advances in Intelligent Systems and Computing).

@inproceedings{93b63ea10eda42569750439d172f3908,

title = "Dissimilar symmetric word pairs in the human genome",

abstract = "In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions. Since symmetric pairs with different patterns could point to evolutionary features, we search for the pairs with the most dissimilar behaviour. We focus our study on the complete human genome and its repeat-masked version.",

keywords = "Dissimilarity measure, Human genome, Inter-word distance, Reversed complements",

author = "Tavares, {Ana Helena} and Jakob Raymaekers and Rousseeuw, {Peter J.} and Silva, {Raquel M.} and Bastos, {Carlos A.C.} and Armando Pinho and Paula Brito and Vera Afreixo",

note = "Funding Information: This work was partially supported by the Portuguese Foundation for Science and Technology (FCT), Center for Research & Development in Mathematics and Applications (CIDMA), Institute of Biomedicine (iBiMED) and Institute of Electronics and Informatics Engineering of Aveiro (IEETA), within projects UID/MAT/04106/2013, UID/BIM/04501/2013 and UID/CEC/00127/2013, and by PhD grant PD/BD/105729/2014. The research of P. Brito was financed by the ERDF -European Regional Development Fund through the Operational Programme for Competitiveness and Internationalisation (COMPETE 2020) within project POCI-01-0145-FEDER-006961, and by the FCT as part of project UID/EEA/50014/2013. The research of J. Raymaekers and P. Rousseeuw was supported by projects of Internal Funds KU Leuven. Publisher Copyright: {\textcopyright} Springer International Publishing AG 2017. Copyright: Copyright 2017 Elsevier B.V., All rights reserved.; 11th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2017 ; Conference date: 21-06-2017 Through 23-06-2017",

year = "2017",

doi = "10.1007/978-3-319-60816-7_30",

language = "English",

isbn = "9783319608150",

series = "Advances in Intelligent Systems and Computing",

publisher = "Springer Verlag",

pages = "248--256",

editor = "Miguel Rocha and {De Paz}, {Juan F.} and Tiago Pinto and Florentino Fdez-Riverola and Mohamad, {Mohd Saberi}",

booktitle = "11th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2017",

address = "Germany",

}

Tavares, AH, Raymaekers, J, Rousseeuw, PJ, Silva, RM, Bastos, CAC, Pinho, A, Brito, P & Afreixo, V 2017, Dissimilar symmetric word pairs in the human genome. in M Rocha, JF De Paz, T Pinto, F Fdez-Riverola & MS Mohamad (eds), 11th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2017. Advances in Intelligent Systems and Computing, vol. 616, Springer Verlag, pp. 248-256, 11th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2017, Porto, Portugal, 21/06/17. https://doi.org/10.1007/978-3-319-60816-7_30

Dissimilar symmetric word pairs in the human genome. / Tavares, Ana Helena; Raymaekers, Jakob; Rousseeuw, Peter J. et al.
11th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2017. ed. / Miguel Rocha; Juan F. De Paz; Tiago Pinto; Florentino Fdez-Riverola; Mohd Saberi Mohamad. Springer Verlag, 2017. p. 248-256 (Advances in Intelligent Systems and Computing; Vol. 616).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Dissimilar symmetric word pairs in the human genome

AU - Tavares, Ana Helena

AU - Raymaekers, Jakob

AU - Rousseeuw, Peter J.

AU - Silva, Raquel M.

AU - Bastos, Carlos A.C.

AU - Pinho, Armando

AU - Brito, Paula

AU - Afreixo, Vera

N1 - Funding Information: This work was partially supported by the Portuguese Foundation for Science and Technology (FCT), Center for Research & Development in Mathematics and Applications (CIDMA), Institute of Biomedicine (iBiMED) and Institute of Electronics and Informatics Engineering of Aveiro (IEETA), within projects UID/MAT/04106/2013, UID/BIM/04501/2013 and UID/CEC/00127/2013, and by PhD grant PD/BD/105729/2014. The research of P. Brito was financed by the ERDF -European Regional Development Fund through the Operational Programme for Competitiveness and Internationalisation (COMPETE 2020) within project POCI-01-0145-FEDER-006961, and by the FCT as part of project UID/EEA/50014/2013. The research of J. Raymaekers and P. Rousseeuw was supported by projects of Internal Funds KU Leuven. Publisher Copyright: © Springer International Publishing AG 2017. Copyright: Copyright 2017 Elsevier B.V., All rights reserved.

PY - 2017

Y1 - 2017

N2 - In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions. Since symmetric pairs with different patterns could point to evolutionary features, we search for the pairs with the most dissimilar behaviour. We focus our study on the complete human genome and its repeat-masked version.

AB - In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions. Since symmetric pairs with different patterns could point to evolutionary features, we search for the pairs with the most dissimilar behaviour. We focus our study on the complete human genome and its repeat-masked version.

KW - Dissimilarity measure

KW - Human genome

KW - Inter-word distance

KW - Reversed complements

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U2 - 10.1007/978-3-319-60816-7_30

DO - 10.1007/978-3-319-60816-7_30

M3 - Conference contribution

AN - SCOPUS:85025122728

SN - 9783319608150

T3 - Advances in Intelligent Systems and Computing

SP - 248

EP - 256

BT - 11th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2017

A2 - Rocha, Miguel

A2 - De Paz, Juan F.

A2 - Pinto, Tiago

A2 - Fdez-Riverola, Florentino

A2 - Mohamad, Mohd Saberi

PB - Springer Verlag

T2 - 11th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2017

Y2 - 21 June 2017 through 23 June 2017

ER -

Tavares AH, Raymaekers J, Rousseeuw PJ, Silva RM, Bastos CAC, Pinho A et al. Dissimilar symmetric word pairs in the human genome. In Rocha M, De Paz JF, Pinto T, Fdez-Riverola F, Mohamad MS, editors, 11th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2017. Springer Verlag. 2017. p. 248-256. (Advances in Intelligent Systems and Computing). doi: 10.1007/978-3-319-60816-7_30

Dissimilar symmetric word pairs in the human genome

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Keywords

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