Genome-Wide Predictions
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Genome-Wide nucleosomes predictions across species



We hereby supply two types of genome-wide nucleosome positioning predictions by our model (The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome, Kaplan et al. 2008) for several organisms. The "Model score" is the score that our model assigns to each 147bp sequence in the genome for the positioning potential of this sequence. The "Average occupancy" is the predicted probability for each position in the genome to be covered by any nucleosome, under an assumed equilibrium between all feasible (i.e., non overlapping) nucleosome configurations.
For yeast, we provide an additional track of log-normalized averaged occupancy: For each basepair, we take the log of the ratio between the basepair's average occupancy and the mean genomic average occupancy; Then, we set the genomic average to zero by subtracting from each basepair the new mean.

  Average occupancyModel scoreGenome sequence
Humanhg17Ucsc
Humanhg18Ucsc
YeastsacCer1   Norm: Ucsc
YeastSgd (Jan 2006)   Norm: Sgd
Mousemm8Ucsc
Mousemm9Ucsc
Flydm3Ucsc
Wormce4Ucsc
PhageLambdaNcbi
Human CMV(Strain TB40)Ncbi
ArabidopsisTAIR8TAIR8
S. PombeSanger (Apr 2010)Sanger

The above predictions are in a tab delimited file (.chv) where each row consists of the following columns:
ChromosomeRegion startRegion endValues list (delimited by semicolon)


Note that the genomic coordinates are 1-based.

We supply a perl script named nucleo08_chv2chr.pl that converts the .chv file to a more standard format:
ChromosomePositionValue


In order to convert a file to the more standard format, first unzip it, then run the script on it:

nucleo08_chv2chr.pl <chv input file name> -o <output file name>

Genomica Genome Browser files


Uncompress and open the yeast chromosome tracks files in Genomica Genome Browser. These chromosome tracks are 10bp window averaging over the predictions. You can download Genomica here.

  Average occupancyModel score
YeastsacCer1
YeastSgd (Jan 2006)