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Nucleosome Prediction Tools

Nucleosome measurements


SpeciesIn-VitroIn-Vivo
C albicans
S cerevisiae*

* This data was published in Kaplan et al, Nature 2008.



The above data is 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>

Raw data (Solexa sequence reads in Fasta file format) for both the C. albicans in-vitro and in-vivo experiments: (1.3GB)

Nucleosome predictions


SpeciesField08Kaplan08
A gossypii
C albicans
C glabrata
D hansenii
K lactis
K waltii
S bayanus
S castellii
S cerevisiae
S mikatae
S paradoxus
Y lipolytica

The predictions are in the same tab delimited file format as the data in the "Nucleosome Measurements" table above.

Gene Categories


SpeciesGene Category IGene Category IIGene Category III
A gossypii
C albicans
C glabrata
D hansenii
K lactis
K waltii
S bayanus
S castellii
S cerevisiae
S mikatae
S paradoxus
Y lipolytica


Additional information


SpeciesGenome SequenceGene LocationOrthogroup Mapping
A gossypii
C albicans
C glabrata
D hansenii
K lactis
K waltii
S bayanus
S castellii
S cerevisiae
S mikatae
S paradoxus
Y lipolytica

The "Gene Location" files are in tab delimited format with 4 columns: Chromosome; Gene Id; Gene start; Gene end.
The "Orthogroup Mapping" files are in tab delimited format with 2 columns: Orthogroup Id; Gene Id.

We thank Ilan Wapinski and Aviv Regev for kindly supplying the orthogroup mapping files, with the corresponding genome sequence and gene location files.