OligoCounter

OligoCounter identifies and quantifies overrepresented octa- to tetradecanucleotide (8-14 bp) sequences in DNA to characterize compositional biases, repeats, genomic islands, and species-specific markers in bacterial genomes.

Key Features:

• Implementation: Java-based implementation for processing DNA sequence data.
• Identification of Overrepresented Oligonucleotides: Detects oligonucleotides that exceed a predefined threshold, focusing on octa- to tetradecanucleotides (8-14 bp).
• Pattern Recognition: Distinguishes distributions in coding versus non-coding regions, where non-coding oligos are often part of longer repeats and coding oligos are distributed through the core genome and align with local tetranucleotide usage patterns.
• Genomic Island Detection: Identifies genomic islands as regions depleted in overrepresented oligonucleotides.
• Species Identification Markers: Highlights frequently occurring coding 8-14mers that appear on average every 10,000 bp or less as potential markers for species identification.
• Metagenomic Read Attribution and Quantification: Scans primary sequence reads from next-generation sequencing to attribute short reads to sequenced genomes and quantify metagenomic composition using 8-14mer markers.
• Genome-scale Visualization: Enables global-scale visualization of small genomes based on oligonucleotide composition.

Scientific Applications:

• Genomic composition analysis: Characterizing oligonucleotide composition to understand bacterial genome organization and evolution.
• Repeat region investigation: Mapping overrepresented oligos to investigate and characterize repeat regions.
• Genomic island identification: Detecting genomic islands via depletion patterns of overrepresented oligonucleotides.
• Species marker discovery: Identifying species-specific 8-14mer markers for species identification.
• Metagenomic attribution and quantification: Attributing and quantifying short reads from next-generation sequencing datasets by scanning for 8-14mer markers.
• Small-genome visualization: Visualizing small genomes at a global scale using oligonucleotide distribution patterns.

Methodology:

Analyzes completely sequenced genomes (e.g., Pseudomonas), systematically searches for highly overrepresented 8-14mers, and categorizes them by distribution in coding versus non-coding regions and by association with repeats and genomic islands.