This article is part of the supplement: The 2008 International Conference on Bioinformatics & Computational Biology (BIOCOMP'08)

Open Access Research

Word-based characterization of promoters involved in human DNA repair pathways

Jens Lichtenberg1*, Edwin Jacox2, Joshua D Welch1, Kyle Kurz1, Xiaoyu Liang1, Mary Q Yang2, Frank Drews1, Klaus Ecker1, Stephen S Lee3, Laura Elnitski2 and Lonnie R Welch1,4,5

1 Bioinformatics Laboratory, School of Electrical Engineering and Computer Science, Ohio University, Athens, Ohio, USA

2 Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, USA

3 Department of Statistics, University of Idaho, Moscow, Idaho, USA

4 Biomedical Engineering Program, Ohio University, Athens, Ohio, USA

5 Molecular and Cellular Biology Program, Ohio University, Athens, Ohio, USA

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BMC Genomics 2009, 10(Suppl 1):S18 doi:10.1186/1471-2164-10-S1-S18

Published: 7 July 2009

Additional files

Additional file 1:

Words discovered in bidirectional promoters. Entire set of words discovered in the bidirectional promoters with occurrences, expected occurrences, scores, reverse complement information and p-value.

Format: CSV Size: 1.4MB Download file

Open Data

Additional file 2:

Words discovered in unidirectional promoters. Entire set of words discovered in the unidirectional promoters with occurrences, expected occurrences, scores, reverse complement information and p-value.

Format: CSV Size: 1.4MB Download file

Open Data

Additional file 3:

Missing words in bidirectional promoters. Set of words not detected in the bidirectional promoters with expected occurrences.

Format: CSV Size: 1.4MB Download file

Open Data

Additional file 4:

Missing words in unidirectional promoters. Set of words not detected in the unidirectional promoters with expected occurrences.

Format: CSV Size: 1.4MB Download file

Open Data

Additional file 5:

Hamming distance clusters in bidirectional promoters. Entire set of hamming distance based clusters for the bidirectional promoters with detailed cluster element information position weight matrix and corresponding regular expression motif.

Format: CSV Size: 68KB Download file

Open Data

Additional file 6:

Hamming distance clusters in unidirectional promoters. Entire set of hamming distance based clusters for the unidirectional promoters with detailed cluster element information position weight matrix and corresponding regular expression motif.

Format: CSV Size: 51KB Download file

Open Data

Additional file 7:

Edit distance clusters in bidirectional promoters. Entire set of edit distance based clusters for the bidirectional promoters with detailed cluster element information position weight matrix and corresponding regular expression motif.

Format: CSV Size: 751KB Download file

Open Data

Additional file 8:

Edit distance clusters in unidirectional promoters. Entire set of edit distance based clusters for the unidirectional promoters with detailed cluster element information position weight matrix and corresponding regular expression motif.

Format: CSV Size: 620KB Download file

Open Data