periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA

Periodic occurrences of oligonucleotide sequences can impact the physical properties of DNA. For example, DNA bendability is modulated by 10-bp periodic occurrences of WW (W = A/T) dinucleotides. We present periodicDNA, an R package to identify k-mer periodicity and generate continuous tracks of k-m...

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Detalles Bibliográficos
Autores principales: Serizay, Jacques, Ahringer, Julie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2021
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8063535/
https://www.ncbi.nlm.nih.gov/pubmed/33953908
http://dx.doi.org/10.12688/f1000research.51143.1
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author Serizay, Jacques
Ahringer, Julie
author_facet Serizay, Jacques
Ahringer, Julie
author_sort Serizay, Jacques
collection PubMed
description Periodic occurrences of oligonucleotide sequences can impact the physical properties of DNA. For example, DNA bendability is modulated by 10-bp periodic occurrences of WW (W = A/T) dinucleotides. We present periodicDNA, an R package to identify k-mer periodicity and generate continuous tracks of k-mer periodicity over genomic loci of interest, such as regulatory elements. periodicDNA will facilitate investigation and improve understanding of how periodic DNA sequence features impact function.
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spelling pubmed-80635352021-05-04 periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA Serizay, Jacques Ahringer, Julie F1000Res Software Tool Article Periodic occurrences of oligonucleotide sequences can impact the physical properties of DNA. For example, DNA bendability is modulated by 10-bp periodic occurrences of WW (W = A/T) dinucleotides. We present periodicDNA, an R package to identify k-mer periodicity and generate continuous tracks of k-mer periodicity over genomic loci of interest, such as regulatory elements. periodicDNA will facilitate investigation and improve understanding of how periodic DNA sequence features impact function. F1000 Research Limited 2021-02-24 /pmc/articles/PMC8063535/ /pubmed/33953908 http://dx.doi.org/10.12688/f1000research.51143.1 Text en Copyright: © 2021 Serizay J and Ahringer J https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Serizay, Jacques
Ahringer, Julie
periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
title periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
title_full periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
title_fullStr periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
title_full_unstemmed periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
title_short periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
title_sort periodicdna: an r/bioconductor package to investigate k-mer periodicity in dna
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8063535/
https://www.ncbi.nlm.nih.gov/pubmed/33953908
http://dx.doi.org/10.12688/f1000research.51143.1
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AT ahringerjulie periodicdnaanrbioconductorpackagetoinvestigatekmerperiodicityindna

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