Research article
Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae
- † Equal contributors
Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, USA
BMC Genomics 2006, 7:276 doi:10.1186/1471-2164-7-276
Published: 26 October 2006Additional files
Additional file 1:
HMM parameters. See Methods for explanation.
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Additional file 2:
ORC-only sites.
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Additional file 3:
MCM2-only sites.
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Additional file 4:
ORC-MCM2 sites.
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Additional file 5:
Identification of known ARS.
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Additional file 12:
Logo of 31 known ACSs demonstrates the EACS+B1 element. The dashed line shows 95% quantile (0.17 bits) of information content distribution of 31 10,000 bp random sequences. Based on the cutoff, we used a 17 bp EACS + 3 bp B1 to construct a gapped PWM to scan nimARS.
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Additional file 6:
Set of nimARS.
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Additional file 10:
Verified nimARS. Coordinates of regions tested for ARS activity are provided. ARS names are assigned to be consistent with Wyrick et al. [24] and the DNA replication origin database [64].
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Additional file 11:
False predictions of Wyrick et al. [24].
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Additional file 7:
Known ACS.
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Additional file 8:
Predicted nimACS.
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Additional file 9:
Verified nimACS.
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Additional file 13:
Normalization using global loess. The red line indicates the loess line. M is the log of ratio of IP divided by total (also termed enrichment score) and A is the average log intensity.
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