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Prediction of Saccharomyces cerevisiae replication origins

Adam M Breier1, Sourav Chatterji2 and Nicholas R Cozzarelli3*

Author Affiliations

1 Graduate Group in Biophysics, University of California-Berkeley, Berkeley, CA 94720-3204, USA

2 Department of Computer Science, University of California-Berkeley, Berkeley, CA 94720-3204, USA

3 Department of Molecular and Cellular Biology, Barker Hall, University of California-Berkeley, Berkeley, CA 94720-3204, USA

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Genome Biology 2004, 5:R22  doi:

Published: 4 March 2004

Additional files

Additional data file 1:

Locations of known origins and ORC/MCM binding sites used in the evaluation and training sets

Format: XLS Size: 63KB Download file

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Additional data file 2:

Position weight matrices used by Oriscan

Format: XLS Size: 84KB Download file

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Additional data file 3:

ACS matches identified by Oriscan

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Additional data file 4:

The ranked list of 1,882 candidate origins that passed the first three steps of Oriscan

Format: XLS Size: 367KB Download file

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Additional data file 5:

ACS and flanking score distributions

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Additional data file 6:

The ARS assay results

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Additional data file 7:

Representative ARS assays

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Additional data file 8:

Sequences of the training set and experimentally supported predictions ranking 350 or better

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Additional data file 9:

The frequency matrix calculated from the sequences in Additional data file 8, and used to generate Figure 6 and Additional data file 10

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Additional data file 10:

A graphical representation of ACS and B1 nucleotide frequencies in all experimentally supported Oriscan predictions and known origins

Format: PDF Size: 12KB Download file

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