NuPoP: Nucleosome Positioning Prediction Engine

Species: DHMM:

Paste your sequence in the box above, or upload a sequence file in FASTA format*:



Please paste in or upload one, and only one, query sequence of length 148-50,000 bp to predict the nucleosome positioning.
For longer sequences, please use the stand-alone Fortran program or NuPoP R package.

*FASTA format requires the first line should be ">sequenceName", each line is of the same length (the last line can be shorter).

About NuPoP

  NuPoP is a software tool for Nucleosome Positioning Prediction. NuPoP is built upon a duration hidden Markov model, in which the linker DNA length is explicitly modeled. The nucleosome or linker DNA state model can be chosen as either a 4th order or 1st orderMarkov chain. NuPoP outputs the Viterbi prediction, nucleosome occupancy score (from backward and forward algorithms) and nucleosome affinity score. NuPoP has three formats including a web server prediction engine, a stand-alone Fortran program, and an R package. The latter two can predict nucleosome positioning for a DNA sequence of any length. NuPoP_F is the Fotran program that allows customized compiling of Fortran codes.

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Reference

For comments, please contact: jzwang@northwestern.edu or j-widom@northwestern.edu. For more information on NuPoP and the methods, please refer to the following papers:
  1. Xi, L., Fondufe-Mittendor, Y., Xia, L., Flatow, J., Widom, J. and Wang, J.-P., Predicting nucleosome positioning using a duration Hidden Markov Model, BMC Bioinformatics, 2010, doi:10.1186/1471-2105-11-346.
  2. Wang, J.-P., Fondufe-Mittendorf, Y., Xi, L., Tsai, G., Segal, E. and Widom, J., Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae, PLoS Computational Biology, 2008, 4(9) e100017
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