kmerPyramid

kmerPyramid projects nucleobase and k-mer frequency distributions from DNA or RNA sequences into a three-dimensional PCA-derived pyramid for visualization and comparative analysis.

Key Features:

• Nucleobase and k-mer frequency calculation: Calculates nucleobase and k-mer frequency distributions for DNA and RNA sequences represented as multi-dimensional frequency matrices (sequences × nucleobases/k-mers).
• Multi-dimensional frequency matrices: Represents sequence composition as frequency matrices with sequences as rows and nucleobases or k-mers as columns.
• Dimensionality reduction (PCA): Applies principal component analysis to project high-dimensional frequency matrices into three principal components while preserving variance.
• 3D pyramid visualization: Maps each sequence to a point within a three-dimensional pyramid derived from the PCA projection to facilitate comparative visualization of composition.
• Reference k-mer datasets: Provides pre-calculated k-mer frequency matrices for approximately 2,000 bacterial and 5,000 viral reference sequences from the NCBI RefSeq GenBank database.

Scientific Applications:

• Metagenomic analysis: Visualizes nucleobase and k-mer distributions to support interpretation of microbial community composition and functional potential in environmental samples.
• Phylogenetic studies: Highlights intra- and inter-species sequence composition differences to aid exploration of evolutionary relationships.
• Comparative genomics: Enables comparison of genomic composition across organisms for studies of biodiversity, adaptation, and pathogen evolution.

Methodology:

Compute nucleobase or k-mer frequencies for input sequences, project the resulting frequency matrices onto principal components via PCA to reduce dimensionality, and place sequences as points within a 3D pyramid visualization.