nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. In nuCpos, a duration hidden Markov model is trained with a chemical map of nucleosomes either from budding yeast (Brogaard et al. (2012)), fission yeast (Moyle-Heyrman et al. (2012)), or mouse embryonic stem cells (Voong et al. (2016)). nuCpos outputs the Viterbi (most probable) path of nucleosome-linker states, predicted nucleosome occupancy scores and histone binding affinity (HBA) scores as NuPoP does. nuCpos can also calculate local and whole nucleosomal HBA scores for a given 147-bp sequence. Furthermore, effect of genetic alterations on nucleosome occupancy can be predicted with this package. The parental package NuPoP, which is based on an MNase-seq-based map of budding yeast nucleosomes, was developed by Ji-Ping Wang and Liqun Xi, licensed under GPL-2. Please refer to Xi et al. (2010) and Wang et al. (2008) for technical details of NuPoP.
predNuCpos: R function for prediction of nucleosome
positioning, nucleosome occupancy and HBA scores.
HBA: R function for calculation of the histone
binding affinity score of a whole nucleosome.
localHBA: R function for calculation of
the local histone binding affinity.
mutNuCpos: R function for predicting the effect of
a genetic alteration on nucleosome positioning.
Hiroaki Kato and Takeshi Urano
Maintainer: Hiroaki Kato<firstname.lastname@example.org>
Wang JP, Fondufe-Mittendorf Y, Xi L, Tsai GF, Segal E and Widom J (2008). Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae. PLoS Computational Biology, 4(9):e1000175.
Xi L, Fondufe-Mittendorf Y, Xia L, Flatow J, Widom J and Wang JP (2010). Predicting nucleosome positioning using a duration hidden markov model. BMC Bioinformatics, 11:346
Brogaard K, Xi L, and Widom J (2012). A map of nucleosome positions in yeast at base-pair resolution. Nature, 486(7404):496-501.
Moyle-Heyrman G, Zaichuk T, Xi L, Zhang Q, Uhlenbeck OC, Holmgren R, Widom J and Wang JP (2013). Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning. Proc. Natl. Acad. Sci. U. S. A., 110(50):20158-63.
Ichikawa Y, Morohoshi K, Nishimura Y, Kurumizaka H and Shimizu M (2014). Telomeric repeats act as nucleosome-disfavouring sequences in vivo. Nucleic Acids Res., 42(3):1541-1552.
Voong LN, Xi L, Sebeson AC, Xiong B, Wang JP and Wang X (2016). Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping. Cell, 167(6):1555-1570.
Fuse T, Katsumata K, Morohoshi K, Mukai Y, Ichikawa Y, Kurumizaka H, Yanagida A, Urano T, Kato H, and Shimizu M (2017). Parallel mapping with site-directed hydroxyl radicals and micrococcal nuclease reveals structural features of positioned nucleosomes in vivo. Plos One, 12(10):e0186974.
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