Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

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

Weihong Xu, Jennifer G Aparicio, Oscar M Aparicio* and Simon Tavaré*

Author Affiliations

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, USA

For all author emails, please log on.

BMC Genomics 2006, 7:276  doi:10.1186/1471-2164-7-276

Published: 26 October 2006

Additional files

Additional file 1:

HMM parameters. See Methods for explanation.

Format: XLS Size: 16KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

ORC-only sites.

Format: XLS Size: 14KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

MCM2-only sites.

Format: XLS Size: 49KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

ORC-MCM2 sites.

Format: XLS Size: 68KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Identification of known ARS.

Format: XLS Size: 81KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

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.

Format: PDF Size: 31KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Set of nimARS.

Format: XLS Size: 117KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

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].

Format: XLS Size: 38KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 11:

False predictions of Wyrick et al. [24].

Format: XLS Size: 12KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Known ACS.

Format: XLS Size: 33KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Predicted nimACS.

Format: XLS Size: 135KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 9:

Verified nimACS.

Format: DOC Size: 63KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

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.

Format: PDF Size: 30KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data