BU ORChID Track Settings
ENCODE Boston Univ (Tullius Lab) ORChID Predicted DNA Cleavage Sites   (All Mapping and Sequencing tracks)

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 Signal  ENCODE Boston Univ. OH Radical Cleavage Intensity Database (ORChID) V1    Schema   2010-10-24 
 Signal  ENCODE Boston Univ. OH Radical Cleavage Intensity Database (ORChID) V2    Schema   2010-10-24 
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This set of tracks displays the predicted hydroxyl radical cleavage intensity on naked DNA for each nucleotide in the genome. Because the hydroxyl radical cleavage intensity is proportional to the solvent accessible surface area of the deoxyribose hydrogen atoms (Balasubramanian et al., 1998), these tracks represent a structural profile of the DNA in the genome.

For additional details, please visit the Tullius lab website.

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In the full and pack display modes, positive intensity values are shown in red and negative intensity values are shown in tan. In the squish and dense display modes, intensity is represented in grayscale (the darker the shading, the higher the intensity).

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Hydroxyl radical cleavage intensity predictions were performed using an in-house sliding tetramer window (STW) algorithm. This algorithm draws data from the ·OH Radical Cleavage Intensity Database (ORChID), which contains more than 150 experimentally determined cleavage patterns. The ORChID Version 1 predictions are performed on the + strand of the DNA sequence. These predictions are fairly accurate, with a Pearson coefficient of 0.88 between the predicted and experimentally determined cleavage intensities. For ORChID Version 2, two predictions are performed, one on the + strand and the other on the - strand, and then the average of the predicted cleavage intensity for nucleotides in close proximity across the minor groove is presented. For more details on the hydroxyl radical cleavage method, see below for reference (Greenbaum et al. 2007).


The STW algorithm has been cross-validated by removing each test sequence from the training set and performing a prediction. The mean correlation coefficient (between predicted and experimental cleavage patterns) from this study was 0.88.


These data were generated at Boston University and NHGRI.

Contact: Tom Tullius

These data are the result of the combined efforts of Bo Pang (now at MIT), Jason Greenbaum (now at The La Jolla Institute for Allergy and Immunology), Steve Parker and Elliott Margulies at The National Human Genome Research Institute, National Institutes of Health, and Eric Bishop and Tom Tullius at Boston University.


Balasubramanian B, Pogozelski WK, and Tullius TD. DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl. Acad. Sci. USA. 1998 Aug 18;95(17):9738-43.

Price MA, and Tullius TD. Using the Hydroxyl Radical to Probe DNA Structure. Meth. Enzymol. 1992;212:194-219.

Tullius TD. Probing DNA Structure with Hydroxyl Radicals. Curr Protoc Nucleic Acid Chem. 2002 Feb;Chapter 6:Unit 6.7. Review.

Greenbaum JA, Pang B, and Tullius TD. Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res. 2007 Jun;17(6):947-53.

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Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here.