Dec 152012
 

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

Dr Colin F. Davenport

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 OligoCounter

:: 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.

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