This web site provides:

  1. A GBrowse view of the S.cerevisiae genome with nucleosome energy and positioning data (includes DNABEND and alignment model I as described in Segal et al., "A genomic code for nucleosome positioning", Nature, 442, 772-778).
  2. Nucleosome energies (log-scores), probabilities, and occupancies computed with DNABEND, alignment model I, and alignment model II for download.
  3. DNABEND and DynaPro software packages for download.

Supporting data For each of the 16 S.cerevisiae chromosomes we provide the following data in the plain text format:

  1. chr??.etable.rescaled.3 - DNABEND energies for each genomic base pair
  2. chr??.occ.3 - DNABEND probabilities and occupancies for each genomic base pair
  3. chr??.etable.eran.mixed - alignment model I log-scores
  4. chr??.eran.mixed.occ - alignment model II probabilities and occupancies
  5. chr??.etable.eran.2.rescaled - alignment model II log-scores
  6. chr??.occ.eran.3 - alignment model II probabilities and occupancies
  7. Scer_chr??.fsa - S.cerevisiae genomic sequence (circa Nov.2005) used in all calculations
All models and terms are defined in the DNABEND paper.


  1. DNABEND_1.1 - uses a DNA mechanics-based biophysical approach to compute DNABEND nucleosome energies from DNA sequence. Last update (with a bug fix - thanks to Kenneth Evans, School of Crystallography, Birkbeck College, London): October, 2007. Please see the README file for installation and usage instructions, including tutorial and worked examples. Both single processor and cluster runs setup instructions and scripts are provided.
  2. DynaPro_1.1 - computes probabilities of placing a DNA-binding factor and resulting factor occupancies for each base pair in the input DNA sequence using a dynamic programming (transfer matrix) approach. Last update: July, 2007. DNA-binding factors include (but are not limited to) histone octamers and transcription factors. DynaPro uses DNABEND output energies for nucleosome calculations and provides tools for computing transcription factor energy landscapes. All energy landscapes are combined by DynaPro to produce nucleosome probability and occupancy profiles in the presence of other DNA-binding factors. Please see the README file for installation and usage instructions, including tutorial and worked examples.

Experimentally known nucleosome locations

    The data on nucleosome positions was collected from the literature (see Supplementary Information from the DNABEND paper for further details), and formatted for easy GBrowse upload. Please download the GFF files and use the "Upload a file" GBrowse field to add them to the list of available tracks. Please refer to GBrowse help for further instructions. Note that these files are designed to be easily modified and augmented by GBrowse users.

Energies and occupancies displayed in GBrowse

    All energies and log-scores are non-negative because we plot (E - Emin) rather than E for each chromosome. Note that the energy scale is arbitrary (see the paper for details). The range of occupancies is between 0 (occupancy=0.0) and 100 (occupancy=1.0). All energies and occupancies are binned and rounded for technical purposes and to facilitate presentation.