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P-clouds specifications

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Unique identifier OMICS_03543
Name P-clouds
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Publications for P-clouds

P-clouds in publications

 (8)
PMCID: 4992247
PMID: 27542599
DOI: 10.1186/s12864-016-3015-5

[…] detect very short sequences. indeed, these methods can be calibrated to be insensitive to the minimum size of repeated sequences as well to their sequence divergence. we selected two such methods, p-clouds [] and red [] (additional file )., the overall proportion of repeats in the galgal4 model detected with p-clouds (33 %) and red (29.9 %) were similar, but were also approximately 50 % higher […]

PMCID: 4746887
PMID: 26862351
DOI: 10.1186/s13100-016-0059-7

[…] the largest component of mammalian genomes [–]; using the repeatmasker approach [, ] it was predicted that approximately half of the human genome is covered by tes, while recent annotation by the p-clouds pipeline suggests the te coverage in human genome may be closer to two-thirds []. most tes of mammals are belong to class i retrotransposons, and the l1 family of lines is still active [–, […]

PMCID: 4675067
PMID: 26653025
DOI: 10.1186/s13059-015-0814-y

[…] i) those bigger than 200 bp were used as probes to run teannot a second time on the genome; ii) those of at least 100 bp and 75 % identity to the cognate consensus sequence were used as input to run p-clouds using 15-mers and the suite of parameters 2, 4, 3, 6, 12. the annotations obtained were combined to calculate repeat density., using as reference the seven pck ancestral chromosomes, […]

PMCID: 4760076
PMID: 26560353
DOI: 10.1093/molbev/msv261

[…] tes. therefore, to get general insights into genomic repetitive content of each lineage or species, 15mer frequencies using 1-fold coverage, quality trimmed read data were calculated following with p-clouds c10 settings (). for lineages of daphnia and leptopilina, the 1-fold coverage amount of read data was used. for mites, the 1-fold read data equivalent of a. coleoptrata was extracted […]

PMCID: 4133154
PMID: 25121584
DOI: 10.1371/journal.pgen.1004482

[…] with less than 80% identity to their human homologue were removed from analysis., we identified lava sequences in the gibbon genome using the probability-based oligonucleotide clustering method p-clouds . the published lava consensus sequence, which contains only the region 3′ of the vntr , was segmented into regions which were used to form clouds. we then searched the genome for locations […]


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P-clouds institution(s)
Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO, USA

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