Abstract
We are studying a generalization of the de Bruijn graphs, with applications to storage. We use spectral methods to enumerate the Euler circuits in this graph, which correspond to (very long) strings accessing every string of fixed length exactly once, with the reader reset at regular intervals. We prove that, when the alphabet is of size q, the subwords considered are of length n and a new reader is initiated every k letters, there are exactly \((q^{k})!^{q^{n} }/q^{k+n}\) such exhaustive words. The enumeration generalizes classic results by Tutte, and relates crucially to subtree enumeration in large networks.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bowe, A., Onodera, T., Sakadane, K., Shibuya, T.: Succinct de Bruijn graphs. In: Algorithms in Bioinformatics. Lecture Notes in Computer Science, pp. 225–235. Springer, Berlin (2012)
Chikhi, R., Rizk, G.: Space-efficient and exact de Bruijn graph representation based on a bloom filter. Algorithms Mol. Biol. 8, 9 (2013)
Compeau, P., Pevzner, P., Tesler, G.: How to apply de Bruijn graphs to genome assembly. Nat. Biotechnol. 29, 987–991 (2011)
Cooper, J., Graham, R.: Generalized de Bruijn cycles (2004). arXiv:0402324
Ehrenborg, R., Kitaev, S., SteingrÃmsson, E.: Number of cycles in the graph of 312-avoiding permutations (2013). arXiv:1310.1520
Flye Saint-Marie, C.: Solution to question 48. l’Intermédiaire des Math. 1, 107–110 (1894)
Lovász, L.: Random walks on graphs: a survey. In: Combinatorics, Paul Erdös is Eighty, pp. 1–46. János Bolyai Mathematical Society, Budapest (1993)
Picoleau, C.: Complexity of the Hamiltonian cycle in regular graph problem. Theor. Comput. Sci. 131(2), 463–473 (1994)
Rödland, E.: Compact representation of k-mer de Bruijn graphs for genome read assembly. BMC Bioinform. 14, 19 (2013)
Rosenfeld, V.: Some spectral properties of the arc-graph. Commun. Math. Comput. Chem. 43, 41–48 (2001)
Rosenfeld, V.: Enumerating de Bruijn sequences. Commun. Math. Comput. Chem. 45, 71–83 (2002)
Stanley, R.: Enumerative Combinatorics, Vol. 2. Cambridge Studies in Advanced Mathematics, vol. 62. Cambridge University Press, New York (1999)
Tutte, W.: The dissection of equilateral triangles into equilateral triangles. Proc. Camb. Philos. Soc. 44, 71–83 (1948)
van Aardenne-Ehrenfest, T., de Bruijn, N.: Circuits and trees in oriented linear graphs. Simon Stevin 28, 143–173 (1951)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Freij, R. (2015). Shifted de Bruijn Graphs. In: Pinto, R., Rocha Malonek, P., Vettori, P. (eds) Coding Theory and Applications. CIM Series in Mathematical Sciences, vol 3. Springer, Cham. https://doi.org/10.1007/978-3-319-17296-5_20
Download citation
DOI: https://doi.org/10.1007/978-3-319-17296-5_20
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-17295-8
Online ISBN: 978-3-319-17296-5
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)