periodicDNA

periodicDNA identifies periodic occurrences of k-mers in DNA sequences, particularly within genomic loci such as regulatory elements.

Key Features:

• k-mer periodicity detection: Identifies periodically occurring k-mers including di- or tri-nucleotides in sets of genomic loci.
• Regulatory element analysis: Provides functions specifically tailored for finding periodic k-mer patterns in DNA sequences such as regulatory elements.
• Distinction from motif spacing analysis: Explicitly excludes identification of motifs separated by a conserved distance, directing users to MEME for such analyses.

Scientific Applications:

• Regulatory genomics: Analysis of periodic sequence patterns in regulatory elements to investigate potential structural or functional roles of k-mer periodicity.
• Genomic loci characterization: Systematic identification of periodic di- and tri-nucleotide patterns across defined sets of genomic regions.

Methodology:

The package provides an R-based approach to find periodic occurrences of k-mers in DNA sequences.