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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. (2007), in review. |
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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. |
References |
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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 .” in review (2007).
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W. Gu, T. A. Castoe, A. P. J. de Koning, D. J. Hedges, M. A. Batzer, and D. D. Pollock, “P-clouds can identify large numbers of novel transposable elements.” in preparation (2007).
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