A pseudo-boolean programming approach for computing the breakpoint distance between two genomes with duplicate genes

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4751 LNBI, Issue , 2007, Pages 16-29

  Angibaud, Sébastien ^a   Fertin, Guillaume ^a   Rusu, Irena ^a   Thévenin, Annelyse ^b   Vialette, Stéphane ^b  

^a UNIVERSITÉ DE NANTES   (France)

^b UFR 919 Laboratoire d'Informatique Pour la Mécanique et les Sciences de l'Ingénieur   (France)

Author keywords

Breakpoint distance; Duplication; Genome rearrangement; Heuristic; Pseudo boolean programming

Indexed keywords

BIOINFORMATICS; BOOLEAN FUNCTIONS; DATA STRUCTURES; ENGINEERING RESEARCH; HEURISTIC PROGRAMMING; PROBLEM SOLVING;

GENOME REARRANGEMENTS; MAXIMUM ADJACENCY DISRUPTION NUMBER (MAD); PSEUDO-BOOLEAN PROGRAMMING;

GENES;

EID: 38349018963     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-74960-8_2     Document Type: Conference Paper

References (18)

1. Angibaud, S., Fertin, G., Rusu, I., Vialette, S.: How pseudo-boolean programming can help genome rearrangement distance computation. In: Bourque, G., El-Mabrouk, N. (eds.) Comparative Genomics. LNCS (LNBI), vol. 4205, pp. 75-86. Springer, Heidelberg (2006)
2. Angibaud, S., Fertin, G., Rusu, I., Vialette, S.: A general framework for computing rearrangement distances between genomes with duplicates. Journal of Computational Biology 14(4), 379-393 (2007)
3. Barth, P.: A Davis-Putnam based enumeration algorithm for linear pseudo-boolean optimization. Technical Report MPI-I-95-2-003, Max Planck Institut Informatik, pages 13 (2005)
4. Blin, G., Chauve, C., Fertin, G.: The breakpoint distance for signed sequences. In: Proc. 1st Algorithms and Computational Methods for Biochemical and Evolutionary Networks (Comp. Bio. Nets.), pp. 3-16. KCL publications (2004)
5. Blin, G., Chauve, C., Fertin, G.: Genes order and phylogenetic reconstruction: Application to γ-proteobacteria. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 11-20. Springer, Heidelberg (2005)
6. Blin, G., Rizzi, R.: Conserved intervals distance computation between non-trivial genomes. In: Wang, L. (ed.) COCOON 2005. LNCS, vol. 3595, pp. 22-31. Springer, Heidelberg (2005)
7. Bourque, G., Yacef, Y., El-Mabrouk, N.: Maximizing synteny blocks to identify ancestral homologs. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 21-35. Springer, Heidelberg (2005)
8. Bryant, D.: The complexity of calculating exemplar distances. In: Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, pp. 207-212. Kluwer Academic Publishers, Dordrecht (2000)
9. Chai, D., Kuehlmann, A.: A fast pseudo-boolean constraint solver. In: Proc. 40th ACM IEEE Conference on Design Automation, pp. 830-835. ACM Press, New York (2003)
10. Chauve, C., Fertin, G., Rizzi, R., Vialette, S.: Genomes containing duplicates are hard to compare. In: Alexandrov, V.N., van Albada, G.D., Sloot, P.M.A., Dongarra, J.J. (eds.) ICCS 2006. LNCS, vol. 3992, pp. 783-790. Springer, Heidelberg (2006)
11. Chen, X., Zheng, J., Fu, Z., Nan, P., Zhong, Y., Lonardi, S., Jiang, T.: Assignment of orthologous genes via genome rearrangement. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2(4), 302-315 (2005)
12. Eén, N., Sörensson, N.: Translating pseudo-boolean constraints into SAT. Journal on Satisfiability, Boolean Modeling and Computation 2, 1-26 (2006)
13. Lerat, E., Daubin, V., Moran, N.A.: From gene tree to organismal phylogeny in prokaryotes: the case of γ-proteobacteria. PLoS Biology 1(1), 101-109 (2003)
14. Marron, M., Swenson, K.M., Moret, B.M.E.: Genomic distances under deletions and insertions. Theoretical Computer Science 325(3), 347-360 (2004)
15. Sankoff, D.: Genome rearrangement with gene families. Bioinformatics 15(11), 909-917 (1999)
16. Sankoff, D., Haque, L.: Power boosts for cluster tests. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 11-20. Springer, Heidelberg (2005)
17. Schrijver, A.: Theory of Linear and Integer Programming. John Wiley and Sons, Chichester (1998)
18. Sheini, H.M., Sakallah, K.A.: Pueblo: A hybrid pseudo-boolean SAT solver. Journal on Satisfiability, Boolean Modeling and Computation 2, 165-189 (2006)