periodicDNA

periodicDNA identifies and analyzes periodic occurrences of k-mers (e.g., di-nucleotides, tri-nucleotides) across genomic loci to assess sequence periodicity and its effects on DNA physical properties such as bendability and 10-base pair WW (W = A/T) periodicity, and is implemented as an R/Bioconductor package.

Key Features:

• K-mer Periodicity Identification: Detects k-mers that recur at regular intervals within sets of genomic sequences, including di-nucleotides and tri-nucleotides.
• Continuous Track Generation: Generates continuous tracks representing k-mer periodicity over specified genomic regions for inspection of pattern distribution across loci.
• Impact on DNA Properties: Quantifies periodic occurrences, including 10-base pair WW (W = A/T) dinucleotide patterns, to relate sequence periodicity to DNA properties such as bendability.

Scientific Applications:

• Regulatory element analysis: Analyzes periodic k-mer patterns within regulatory elements and other genomic loci to investigate potential structural or functional roles.
• DNA structural-function studies: Relates k-mer periodicity (for example, 10-bp WW dinucleotide repeats) to DNA bendability and other physical characteristics that may influence genomic function.

Methodology:

Computational analysis implemented in R/Bioconductor to identify k-mer periodicity within genomic sequences and to generate continuous periodicity tracks over specified genomic regions.