DNA word analysis based on the distribution of the distances between symmetric words

Abstract We address the problem of discovering pairs of symmetric genomic words (i.e., words and the corresponding reversed complements) occurring at distances that are overrepresented. For this purpose, we developed new procedures to identify symmetric word pairs with uncommon empirical distance di...

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Autores principales:	Ana H. M. P. Tavares, Armando J. Pinho, Raquel M. Silva, João M. O. S. Rodrigues, Carlos A. C. Bastos, Paulo J. S. G. Ferreira, Vera Afreixo
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/51c7b6a8aff94a299990323f68956312
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spelling	oai:doaj.org-article:51c7b6a8aff94a299990323f689563122021-12-02T12:32:56ZDNA word analysis based on the distribution of the distances between symmetric words10.1038/s41598-017-00646-22045-2322https://doaj.org/article/51c7b6a8aff94a299990323f689563122017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00646-2https://doaj.org/toc/2045-2322Abstract We address the problem of discovering pairs of symmetric genomic words (i.e., words and the corresponding reversed complements) occurring at distances that are overrepresented. For this purpose, we developed new procedures to identify symmetric word pairs with uncommon empirical distance distribution and with clusters of overrepresented short distances. We speculate that patterns of overrepresentation of short distances between symmetric word pairs may allow the occurrence of non-standard DNA conformations, such as hairpin/cruciform structures. We focused on the human genome, and analysed both the complete genome as well as a version with known repetitive sequences masked out. We reported several well-defined features in the distributions of distances, which can be classified into three different profiles, showing enrichment in distinct distance ranges. We analysed in greater detail certain pairs of symmetric words of length seven, found by our procedure, characterised by the surprising fact that they occur at single distances more frequently than expected.Ana H. M. P. TavaresArmando J. PinhoRaquel M. SilvaJoão M. O. S. RodriguesCarlos A. C. BastosPaulo J. S. G. FerreiraVera AfreixoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ana H. M. P. Tavares Armando J. Pinho Raquel M. Silva João M. O. S. Rodrigues Carlos A. C. Bastos Paulo J. S. G. Ferreira Vera Afreixo DNA word analysis based on the distribution of the distances between symmetric words
description	Abstract We address the problem of discovering pairs of symmetric genomic words (i.e., words and the corresponding reversed complements) occurring at distances that are overrepresented. For this purpose, we developed new procedures to identify symmetric word pairs with uncommon empirical distance distribution and with clusters of overrepresented short distances. We speculate that patterns of overrepresentation of short distances between symmetric word pairs may allow the occurrence of non-standard DNA conformations, such as hairpin/cruciform structures. We focused on the human genome, and analysed both the complete genome as well as a version with known repetitive sequences masked out. We reported several well-defined features in the distributions of distances, which can be classified into three different profiles, showing enrichment in distinct distance ranges. We analysed in greater detail certain pairs of symmetric words of length seven, found by our procedure, characterised by the surprising fact that they occur at single distances more frequently than expected.
format	article
author	Ana H. M. P. Tavares Armando J. Pinho Raquel M. Silva João M. O. S. Rodrigues Carlos A. C. Bastos Paulo J. S. G. Ferreira Vera Afreixo
author_facet	Ana H. M. P. Tavares Armando J. Pinho Raquel M. Silva João M. O. S. Rodrigues Carlos A. C. Bastos Paulo J. S. G. Ferreira Vera Afreixo
author_sort	Ana H. M. P. Tavares
title	DNA word analysis based on the distribution of the distances between symmetric words
title_short	DNA word analysis based on the distribution of the distances between symmetric words
title_full	DNA word analysis based on the distribution of the distances between symmetric words
title_fullStr	DNA word analysis based on the distribution of the distances between symmetric words
title_full_unstemmed	DNA word analysis based on the distribution of the distances between symmetric words
title_sort	dna word analysis based on the distribution of the distances between symmetric words
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/51c7b6a8aff94a299990323f68956312
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DNA word analysis based on the distribution of the distances between symmetric words

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