Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae

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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