OligoCounter 0.64
:: DESCRIPTION
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.
OligoViz : allows direct visualisation of OligoCounter data
OligoWords : generates 4mer data for JCircleGraph (use the perl script to extract 4mer data from a fasta file).
JCircleGraph : visualisation of 4mer and OligoCounter data in attractive genome atlases (requires 4mer files from OligoWords!).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows / Linux / MacOsX
- Java
:: DOWNLOAD
:: MORE INFORMATION
Citation
Davenport, C. F., Wiehlmann, L., Reva, O. N. & Tümmler, B.
Visualization of Pseudomonas genomic structure by abundant 8-14mer oligonucleotides.
Environ Microbiol. 2009 May;11(5):1092-104.