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Open Access Research article

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

Zhandong Liu1, Santosh S Venkatesh2 and Carlo C Maley13*

Author Affiliations

1 Genomics and Computational Biology Graduate Group, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA

2 Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA

3 Systems Biology Division, Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104, USA

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BMC Genomics 2008, 9:509  doi:10.1186/1471-2164-9-509

Published: 30 October 2008

Additional files

Additional file 1:

Supplementary-1. Space coverage of n-mer space (1–20) for Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, and Escherichia coli (K-12) genomes by the stochastic searching algorithm.

Format: TXT Size: 5KB Download file

Open Data

Additional file 2:

Supplementary-2. The 10-mer space coverage for 433 fully sequenced microbial with genomes GC content and genome sizes.

Format: TXT Size: 24KB Download file

Open Data

Additional file 3:

A full list of high frequency n-mers for Homo sapiens genome.

Format: ZIP Size: 1.4MB Download file

Open Data

Additional file 4:

Supplementary-4. The NCBI genome sequence accession ID for Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Saccharomyces cerevisiae.

Format: TXT Size: 1KB Download file

Open Data

Additional file 5:

Supplementary-5. The NCBI genome sequence accession ID for 433 microbial.

Format: TXT Size: 69KB Download file

Open Data