Abstract
This chapter approaches these sorts of questions from three different perspectives, all of which are united by considering words. These are short strings of letters drawn from an alphabet, which in the case of DNA is the set of letters A, C, G, and T. A word of length k is called a “k-word” or “k-tuple”; we use these terms interchangeably. For example, individual bases are 1-tuples, dinucleotides are 2-tuples, and codons are triplets, or 3-tuples. GGGT is a 4-word or 4-tuple.
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References
Campbell AM, Mrázek J, Karlin S (1999) Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proceedings of the National Academy of Sciences USA 96:9184–9189.
Derive™ 5. See http://education.ti.com/us/product/software/derive/features/features.html
Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge: Cambridge University Press.
Karlin S, Campbell AM, Mrázek J (1998) Comparative DNA analysis across diverse genomes. Annual Review of Genetics 32:185–225.
Médigue C, Rouxel T, Vigier P, Hénaut A, Danchin A (1991) Evidence for horizontal gene transfer in Escherichia coli speciation. Journal of Molecular Biology 222:851–856.
Sharp PM, Li W-H (1987) The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research 15:1281–1295.
Whittam TS (1996) In Neidhardt FC (Ed. in Chief), Curtiss III R, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds). Escherichia coli and Salmonella: Cellular and Molecular Biology. Washington, D.C.: ASM Press, pp 2708–2720.
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(2005). Words. In: Computational Genome Analysis. Springer, New York, NY. https://doi.org/10.1007/0-387-28807-4_2
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DOI: https://doi.org/10.1007/0-387-28807-4_2
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