Genomic Signatures in De Bruijn Chains
Genomes have both deterministic and random aspects, with the underlying DNA sequences exhibiting features at numerous scales, from codons to regions of conserved or divergent gene order. This work examines the unique manner in which oligonucleotides fit together to comprise a genome, within a graph-theoretic setting. A de Bruijn chain (DBC) is a generalization of a finite Markov chain. A DNA word graph (DWG) is a generalization of a de Bruijn graph that records the occurrence counts of node and edges in a genomic sequence generated by a DBC. We combine the properties of DWGs and DBCs to obtain a powerful genomic signature demonstrated as information-rich, efficient, and sufficiently representative of the sequence from which it is derived. We illustrate its practical value in distinguishing genomic sequences and predicting the origin of short DNA sequences of unknown origin, while highlighting its superior performance compared to existing genomic signatures including the dinucleotides odds ratio.
KeywordsCodon Bias Genomic Signature Edge Deletion Vertex Deletion Chaos Game Representation
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- 3.Deschavanne, P.J., Giron, A., Vilain, J., Fagot, G., Fertil, B.: Genomic signature: Characterization and classification of species assessed by chaos game representation of sequences. Molecular Biology and Evolution 16(10), 1391–1399 (1999)Google Scholar
- 4.Dufraigne, C., Fertil, B., Lespinats, S., Giron, A., Deschavanne, P.: Detection and characterization of horizontal transfers in prokaryotes using genomic signature. Nucleic Acids Research 33(1), 12 pages (2005)Google Scholar
- 5.Fertil, B., Massin, M., Lespinats, S., Devic, C., Dumee, P., Giron, A.: GENSTYLE: exploration and analysis of DNA sequences with genomic signature. Nucleic Acids Research 33(Web Server issue), W512–W515 (2005)Google Scholar
- 6.Jernigan, R.W., Baran, R.H.: Pervasive properties of the genomic signature. BMC Genomics 3, 9 pages (2002)Google Scholar
- 8.Karlin, S., Mrazek, J., Campbell, A.M.: Compositional biases of bacterial genomes and evolutionary implications. Journal of Bacteriology 179(12), 3899–3913 (1997)Google Scholar
- 17.Heath, L.S., Pati, A.: Genomic signatures from DNA word graphs. LNCS (LNBI), vol. 4463, pp. 317–328. Springer, Heidelberg (2007)Google Scholar
- 19.Rosenberg, A.L., Heath, L.S.: Graph Separators, With Applications. Frontiers of Computer Science. Kluwer Academic/Plenum Publishers, Dordrecht (2000)Google Scholar