Fixed-parameter algorithm for general pedigrees with a single pair of sites

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

Volumn 6053 LNBI, Issue , 2010, Pages 29-37

  Doan, Duong D ^a   Evans, Patricia A ^a  

^a UNIVERSITY OF NEW BRUNSWICK   (Canada)

Author keywords

Fixed parameter algorithm; Haplotyping; Pedigree

Indexed keywords

BIPARTIZATION; EXACT ALGORITHMS; FIXED-PARAMETER ALGORITHMS; HAPLOTYPING; NP-HARD PROBLEM; RECOMBINATION EVENTS;

ALGORITHMS; BIOINFORMATICS;

PARAMETER ESTIMATION;

EID: 77953730721     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-13078-6_5     Document Type: Conference Paper

References (17)

1. Chan, B.M.-Y., Chan, J.W.-T., Chin, F.Y.-L., Fung, S.P.-Y., Kao, M.-Y.: Lineartime haplotype inference on pedigrees without recombinations. In: Bücher, P., Moret, B.M.E. (eds.)WABI 2006. LNCS, vol.4175, pp. 56-67. Springer, Heidelberg (2006)
2. Doan, D.D., Evans, P.A., Horton, J.D.: A Near-Linear Time Algorithm for Haplotype Determination on General Pedigrees. Submitted to Journal of Computational Biology (2009) Submission ID: JCB-2009-10133
3. Downey, R.G., Fellows, M.R.: Parameterized Complexity. Springer, Heidelberg (1999)
4. Guo, J., Gramm, J., Hüffner, F., Niedermeier, R., Wernicke, S.: Compression- Based Fixed-Parameter Algorithms for Feedback Vertex Set and Edge Bipartization. Journal of Computer and System Sciences 72(8), 1386-1396 (2006)
5. Gusfield, D.: An overview of combinatorial methods for haplotype inference. In: Istrail, S., Waterman, M.S., Clark, A. (eds.) DIMACS/RECOMB Satellite Workshop 2002. LNCS (LNBI), vol.2983, pp. 9-25. Springer, Heidelberg (2004)
6. Karp, R.M.: Reducibility Among Combinatorial Problems. In: Miller, R.E., Thatcher, J.W. (eds.) Complexity of Computer Computations, pp. 85-103. Plenum, New York (1972)
7. Li, J., Jiang, T.: Efficient inference of haplotypes from genotypes on a pedigree. Jornal of Bioinformatics and Computational Biology 1(1), 41-70 (2003)
8. Li, J., Jiang, T.: Efficient rule-based haplotyping algorithms for pedigree data. In: Proceedings of Research in Computational Molecular Biology (RECOMB 2003), pp. 197-206. ACM Press, New York (2003)
9. Li, J., Jiang, T.: An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming. In: Proceedings of Research in Computational Molecular Biology (RECOMB 2004), pp. 20-29. ACM Press, New York (2004)
10. Liu, L., Chen, X., Xiao, J., Jiang, T.: Complexity and approximation of the minimum recombinant haplotype configuration problem. Theoretical Computer Science 378, 316-330 (2007)
11. Niedermeier, R.: Invitation to Fixed-Parameter Algorithms. Oxford University Press, Oxford (2006)
12. Qian, D., Beckmann, L.: Minimum-recombinant haplotyping in pedigrees. American Journal of Human Genetics 70(6), 1434-1445 (2002)
13. Reed, B., Smith, K., Vetta, A.: Finding odd cycle transversals. Operations Research Letters 32, 299-301 (2004)
14. Wernicke, S.: On the algorithmic tractability of single nucleotide polymorphism (SNP) analysis and related problems. Diplomarbeit, Wilhelm-Schickard-Institut für Informatik, Universität Tübingen (2003)
15. Xiao, J., Liu, L., Xia, L., Jiang, T.: Fast elimination of redundant linear equations and reconstruction of recombination-free mendelian inheritance on a pedigree. In: Proceedings of the eighteenth annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2007), pp. 655-664 (2007)
16. Xu, S.: The line index and minimum cut of weighted graphs. European Journal of Operational Research 109, 672-682 (1998)
17. Zhang, K., Sun, F., Zhao, H.: HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics 21(1), 90-103 (2005)