Departmental Papers (ESE)


Background: Genomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes.

Results: We have analyzed aspects of the information content of Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, and Escherichia coli (K-12) genomes. Virtually all possible (> 98%) 12 bp oligomers appear in vertebrate genomes while < 2% of 19 bp oligomers are present. Other species showed different ranges of > 98% to < 2% of possible oligomers in D. melanogaster (12-17 bp), C. elegans (11-17 bp), A. thaliana (11-17 bp), S. cerevisiae (10-16 bp) and E. coli (9-15 bp). Frequencies of unique oligomers in the genomes follow similar patterns. We identified a set of 2.6 M 15-mers that are more than 1 nucleotide different from all 15-mers in the human genome and so could be used as probes to detect microbes in human samples. In a human sample, these probes would detect 100% of the 433 currently fully sequenced prokaryotes and 75% of the 3065 fully sequenced viruses. The human genome is significantly more compact in sequence space than a random genome. We identified the most frequent 5- to 20-mers in the human genome, which may prove useful as PCR primers. We also identified a bacterium, Anaeromyxobacter dehalogenans, which has an exceptionally low diversity of oligomers given the size of its genome and its GC content. The entropy of coding regions in the human genome is significantly higher than non-coding regions and chromosomes. However chromosomes 1, 2, 9, 12 and 14 have a relatively high proportion of coding DNA without high entropy, and chromosome 20 is the opposite with a low frequency of coding regions but relatively high entropy.

Conclusion: Measures of the frequency of oligomers are useful for designing PCR assays and for identifying chromosomes and organisms with hidden structure that had not been previously recognized. This information may be used to detect novel microbes in human tissues.

Document Type

Journal Article

Date of this Version



Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples. Zhandong Liu, Santosh S Venkatesh and Carlo C Maley. BMC Genomics 2008, 9:509doi:10.1186/1471-2164-9-509

This article is provided under the terms of this BioMed Central Open Access License. The Work is protected by copyright and/or other applicable law. Any use of the work other than as authorized under this license is prohibited.

By exercising any rights to the Work provided here, you accept and agree to be bound by the terms of this license. The Licensor grants you the rights contained here in consideration of your acceptance of such terms and conditions.”

Reprinted from BMC Genomics, Volume 9, Article Number 509, October 30, 2008





Date Posted: 26 May 2009

This document has been peer reviewed.