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OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. These oligos can be useful in visualising small genomes on a global basis (see figure below), investigating repeats at certain regions, and for attributing short reads (for example from metagenomics) to a sequenced genome.

Simple text output is produced which can be visualised with a suite of associated Java applications, for example JCircleGraph or OligoViz.

A simple explanation of how OligoCounter works is presented here.

For a fully detailed paper on the capabilities of OligoCounter refer to Davenport et al. 2009 (Environmental Microbiology, 2009 11:1092-1104, PMID: 19161433).

OligoCounter is a stable release (providing appropriate input files which closely mimic the NCBI RefSeq format) which was developed and is now maintained by Colin Davenport from the Tümmler lab at Hannover Medical School, Germany.

Pseudomonas aeruginosa

Last modified: 8.12.2009