Description

The P-clouds package is designed to identify repeat structure in large eukaryotic genomes using oligonucleotide counts. It works efficiently on a single desktop computer with 1 Gb memory. The basic program is described in Gu et al. (2008), below.

Downloading

A Linux executable is available here (includes manual and sample control file).

Sample files include input and output (P-cloud assignment, annotation, oligo counts, P-cloud information) for the human X chromosome.

All files are compressed in .zip format.

Source code is intended to be released in the near future.

Manual

Available here. It is pretty brief at this time, so please contact us with questions or requests.

Credits

Original concept by W Gu and D Pollock, programming by W Gu and A.P.J de Koning.

References

• W. Gu, T. A. Castoe, D. J. Hedges, M. A. Batzer, and D. D. Pollock, “Identification of repeat structure in large genomes using repeat probability clouds .”Anal Biochem. 2008 Sep 1;380(1):77-83. Epub 2008 May 20.

• A. P. J. de Koning, W. Gu, T. A. Castoe, M. A. Batzer, and D. D. Pollock, “Repetitive elements may comprise over two-thirds of the
  human genome.” Plos Genetics, in press (2011).