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

Published version
Peer-reviewed

Type

Article

Change log

Authors

Ahringer, Julie 

Abstract

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.

Description

Funder: Medical Research Council

Keywords

DNA periodicity, gene regulation, promoter, DNA, Genome, Genomics, Sequence Analysis, DNA

Journal Title

F1000Res

Conference Name

Journal ISSN

2046-1402
2046-1402

Volume Title

10

Publisher

F1000 Research Ltd
Sponsorship
Wellcome Trust (101863/Z/13/Z)
Medical Research Council (1826632)