Integer linear programs for discovering approximate gene clusters

Rahmann S, Klau GW (2006)
In: Algorithms in Bioinformatics. WABI 2006. Bücher P, Moret BME (Eds); Lecture Notes in Computer Science, 4175. Berlin: Springer: 298-309.

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Konferenzbeitrag | Veröffentlicht | Englisch
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Abstract / Bemerkung
We contribute to the discussion about the concept of approximate conserved gene clusters by presenting a class of definitions that (1) can be written as integer linear programs (ILPs) and () allow several variations that include existing definitions such as common intervals, r-windows, and max-gap clusters or gene teams. While the ILP formulation does not directly lead to optimal algorithms, it provides unprecedented generality and is competitive in practice for those cases where efficient algorithms axe known. It allows for the first time a non-heuristic study of large approximate clusters in several genomes. Source code and datasets are available at http://gi.cebitec.uni-bielefeld.de/assb.
Erscheinungsjahr
Titel des Konferenzbandes
Algorithms in Bioinformatics. WABI 2006
Band
4175
Seite(n)
298-309
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Rahmann S, Klau GW. Integer linear programs for discovering approximate gene clusters. In: Bücher P, Moret BME, eds. Algorithms in Bioinformatics. WABI 2006. Lecture Notes in Computer Science. Vol 4175. Berlin: Springer; 2006: 298-309.
Rahmann, S., & Klau, G. W. (2006). Integer linear programs for discovering approximate gene clusters. In P. Bücher & B. M. E. Moret (Eds.), Lecture Notes in Computer Science: Vol. 4175. Algorithms in Bioinformatics. WABI 2006 (pp. 298-309). Berlin: Springer. doi:10.1007/11851561_28
Rahmann, S., and Klau, G. W. (2006). “Integer linear programs for discovering approximate gene clusters” in Algorithms in Bioinformatics. WABI 2006, Bücher, P., and Moret, B. M. E. eds. Lecture Notes in Computer Science, vol. 4175, (Berlin: Springer), 298-309.
Rahmann, S., & Klau, G.W., 2006. Integer linear programs for discovering approximate gene clusters. In P. Bücher & B. M. E. Moret, eds. Algorithms in Bioinformatics. WABI 2006. Lecture Notes in Computer Science. no.4175 Berlin: Springer, pp. 298-309.
S. Rahmann and G.W. Klau, “Integer linear programs for discovering approximate gene clusters”, Algorithms in Bioinformatics. WABI 2006, P. Bücher and B.M.E. Moret, eds., Lecture Notes in Computer Science, vol. 4175, Berlin: Springer, 2006, pp.298-309.
Rahmann, S., Klau, G.W.: Integer linear programs for discovering approximate gene clusters. In: Bücher, P. and Moret, B.M.E. (eds.) Algorithms in Bioinformatics. WABI 2006. Lecture Notes in Computer Science. 4175, p. 298-309. Springer, Berlin (2006).
Rahmann, Sven, and Klau, Gunnar W. “Integer linear programs for discovering approximate gene clusters”. Algorithms in Bioinformatics. WABI 2006. Ed. P. Bücher and B.M.E. Moret. Berlin: Springer, 2006.Vol. 4175. Lecture Notes in Computer Science. 298-309.