Distribution of distances between symmetric words in the human genome: analysis of regular peaks

Carlos A. C. Bastos; Vera Afreixo; João M. O. S. Rodrigues; Armando J. Pinho; Raquel M. Silva

doi:10.1007/s12539-019-00326-x

Distribution of distances between symmetric words in the human genome: analysis of regular peaks

Carlos A. C. Bastos^*, Vera Afreixo, João M. O. S. Rodrigues, Armando J. Pinho, Raquel M. Silva

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

Finding DNA sites with high potential for the formation of hairpin/cruciform structures is an important task. Previous works studied the distances between adjacent reversed complement words (symmetric word pairs) and also for non-adjacent words. It was observed that for some words a few distances were favoured (peaks) and that in some distributions there was strong peak regularity. The present work extends previous studies, by improving the detection and characterization of peak regularities in the symmetric word pairs distance distributions of the human genome. This work also analyzes the location of the sequences that originate the observed strong peak periodicity in the distance distribution. The results obtained in this work may indicate genomic sites with potential for the formation of hairpin/cruciform structures.

Original language	English
Pages (from-to)	367-372
Number of pages	6
Journal	Interdisciplinary Sciences: Computational Life Sciences
Volume	11
Issue number	3
DOIs	https://doi.org/10.1007/s12539-019-00326-x
Publication status	Published - 1 Sept 2019
Externally published	Yes

Keywords

Cruciform
Distance distribution
Genomic word
Inverted repeats
Regular peaks
Reversed complements

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10.1007/s12539-019-00326-x

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title = "Distribution of distances between symmetric words in the human genome: analysis of regular peaks",

abstract = "Finding DNA sites with high potential for the formation of hairpin/cruciform structures is an important task. Previous works studied the distances between adjacent reversed complement words (symmetric word pairs) and also for non-adjacent words. It was observed that for some words a few distances were favoured (peaks) and that in some distributions there was strong peak regularity. The present work extends previous studies, by improving the detection and characterization of peak regularities in the symmetric word pairs distance distributions of the human genome. This work also analyzes the location of the sequences that originate the observed strong peak periodicity in the distance distribution. The results obtained in this work may indicate genomic sites with potential for the formation of hairpin/cruciform structures.",

keywords = "Cruciform, Distance distribution, Genomic word, Inverted repeats, Regular peaks, Reversed complements",

author = "Bastos, {Carlos A. C.} and Vera Afreixo and Rodrigues, {Jo{\~a}o M. O. S.} and Pinho, {Armando J.} and Silva, {Raquel M.}",

note = "Funding Information: This work was supported by FEDER (“Programa Operacional Fatores de Competitividade”—COMPETE) and by National Funds through FCT (“Funda{\c c}{\~a}o para a Ci{\^e}ncia e a Tecnologia”), within the projects UID/MAT/04106/2013 to CIDMA (Center for Research and Development in Mathematics and Applications), UID/CEC/00127/2013 to IEETA (Institute of Electronics and Informatics Engineering of Aveiro) , UID/BIM/04501/2013 and POCI-01-0145-FEDER-007628 to iBiMED, and the Grant SFRH/BPD/111148/2015 to RMS. Publisher Copyright: {\textcopyright} 2019, International Association of Scientists in the Interdisciplinary Areas. Copyright: Copyright 2019 Elsevier B.V., All rights reserved.",

year = "2019",

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doi = "10.1007/s12539-019-00326-x",

language = "English",

volume = "11",

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journal = "Interdisciplinary Sciences: Computational Life Sciences",

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AU - Bastos, Carlos A. C.

AU - Afreixo, Vera

AU - Rodrigues, João M. O. S.

AU - Pinho, Armando J.

AU - Silva, Raquel M.

N1 - Funding Information: This work was supported by FEDER (“Programa Operacional Fatores de Competitividade”—COMPETE) and by National Funds through 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), UID/CEC/00127/2013 to IEETA (Institute of Electronics and Informatics Engineering of Aveiro) , UID/BIM/04501/2013 and POCI-01-0145-FEDER-007628 to iBiMED, and the Grant SFRH/BPD/111148/2015 to RMS. Publisher Copyright: © 2019, International Association of Scientists in the Interdisciplinary Areas. Copyright: Copyright 2019 Elsevier B.V., All rights reserved.

PY - 2019/9/1

Y1 - 2019/9/1

N2 - Finding DNA sites with high potential for the formation of hairpin/cruciform structures is an important task. Previous works studied the distances between adjacent reversed complement words (symmetric word pairs) and also for non-adjacent words. It was observed that for some words a few distances were favoured (peaks) and that in some distributions there was strong peak regularity. The present work extends previous studies, by improving the detection and characterization of peak regularities in the symmetric word pairs distance distributions of the human genome. This work also analyzes the location of the sequences that originate the observed strong peak periodicity in the distance distribution. The results obtained in this work may indicate genomic sites with potential for the formation of hairpin/cruciform structures.

AB - Finding DNA sites with high potential for the formation of hairpin/cruciform structures is an important task. Previous works studied the distances between adjacent reversed complement words (symmetric word pairs) and also for non-adjacent words. It was observed that for some words a few distances were favoured (peaks) and that in some distributions there was strong peak regularity. The present work extends previous studies, by improving the detection and characterization of peak regularities in the symmetric word pairs distance distributions of the human genome. This work also analyzes the location of the sequences that originate the observed strong peak periodicity in the distance distribution. The results obtained in this work may indicate genomic sites with potential for the formation of hairpin/cruciform structures.

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KW - Distance distribution

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KW - Inverted repeats

KW - Regular peaks

KW - Reversed complements

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Distribution of distances between symmetric words in the human genome: analysis of regular peaks

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Keywords

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