Maintainer: Ji-Ping Wang, <>

References for methods:

  1. Wang, J.-P., Fondufe-Mittendorf, Y., Xi, L., Tsai, G.-F., Segal, E., and Widom, J. (2008). Preferentially quantized linker {DNA} lengths in Saccharomyces cerevisiae. PLoS Computational Biology, 4(9):e1000175.
  2. Xi, L., Fondufe-Mittendorf, Y., Xia, L., Flatow, J., Widom, J., and Wang, J.-P. (2010). Predicting nucleosome positioning using a duration hidden markov model. BMC Bioinformatics, pages doi:10.1186/1471--2105--11--346.
  3. Xi, L., Brogaard,K., Zhang, Q., Lindsay, B.G., Widom, and Wang, J.-P., A locally convoluted cluster model for nucleosome positioning signals in chemical map, Journal of American Statistical Association, 2013, 109(505) 48-62

References for chemical map data used:

  1. Brogaard, K., Xi, L., Wang, J.-P. and Widom, J. (2012), A base pair resolution map of nucleosome positions in yeast, Nature, 2012, 486: 496–501
  2. Moyle-Heyrman, G., Zaichuk, T., Xi, L., Zhang, Q., Uhlenbeck, O.C., Holmgren, R., Widom, J. and Wang, J.-P., Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning, PNAS , 2013,110(50),20158-20163
  3. Voong, L.N, Xi, L., Sebeson, A.C., Xiong, B., Wang, J.-P., Wang, X. Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping , Cell, 2016, 167(6),1555-1570.e15

Version 2 hightlights

NuPoP V2 added a funciton predNuPoP_chem for prediction of nucleosomes using profiles trained based on chemical maps of nucleosomes for yeast, pombe, mouse and human (profiles for other species are extrapolated based on yeast profile). To show a clear improvement, the following figure compares the prediction based on MNase profile vs chemical profile for yeast where the red curve super-imposed is the occupancy from the chemical map for yeast data.