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How OligoCounter works

OligoCounter runs through a simple fasta sequence (.fna format) with a step size of 1 bp, comparing all 8-14bp words with those in memory and counting all oligos which appear.

This is illustrated graphically in the figure below:


Chi-squared statistics are then used to restrict the dataset to interesting words. Overrepresented words found in this way can reveal interesting repeat regions and widespread coding motifs in the investigated genomes. See the documentation for a full explanation.