Islands of tractability for parsimony haplotyping

Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005

Volumn 2005, Issue , 2005, Pages 65-72

  Sharan, Roded ^a   Halldórsson, Bjarni V ^b   Istrail, Sorin ^c  

^a TEL AVIV UNIVERSITY   (Israel)

^b DECODE GENETICS   (Iceland)

^c CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Approximation algorithm; Complexity; Fixed parameter tractability; Genotype; Haplotype inference; Parsimony

Indexed keywords

FIXED PARAMETER TRACTABILITY; GENOTYPE; HAPLOTYPE INFERENCE; PARSIMONY;

ALGORITHMS; APPROXIMATION THEORY; COMPUTATIONAL COMPLEXITY; COMPUTATIONAL METHODS; GENES; POLYNOMIAL APPROXIMATION; PROBLEM SOLVING;

GENETIC ENGINEERING;

ALGORITHM; ARTICLE; CHROMOSOME MAP; DNA SEQUENCE; GENETICS; GENOMIC ISLAND; GENOTYPE; HAPLOTYPE; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; GENOMIC ISLANDS; GENOTYPE; HAPLOTYPES; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 33745480381     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2005.37     Document Type: Conference Paper

References (21)

1. V. Bafna, D. Gusfield, G. Lancia, and S. Yooseph. Haplotyping as a perfect phylogeny. A direct approach. Journal of Computational. Biology, 10(3):323-340, 2003.
2. H. L. Bodlaender. A linear time algorithm for finding tree-decompositions of small treewidth. SIAM Journal on Computing, 25:1305-1317, 1996.
3. A. G. Clark. Inference of haplotypes from PCR-amplified samples of diploid populations. Molecular Biology and Evolution, 7(2): 111-122, 1990.
4. L. Excoffier and M. Slatkin. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Molecular Biology and Evolution, 12(5):921-927, 1995.
5. D. Fallin and N. Schork. Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. American Journal of Human Genetics, 67(4):947-59, 2000.
6. M. R. Garey and D. S. Johnson. Computers and Intractability: A Guide to the Theory of NP-completeness. W.H. Freeman and Company, 1979.
7. G. Greenspan and D. Geiger. Model-based inference of haplotype block variation. Journal of Computational Biology, 11:493-504, 2004.
8. D. Gusfield. A practical algorithm for optimal inference of haplotypes from diploid populations. In Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (ISMB), pages 183-189, 2000.
9. D. Gusfield. Inference of haplotypes from samples of diploid populations: Complexity and algorithms. Journal of Computational Biology, 8(3): 305-324, 2001.
10. D. Gusfield. Haplotyping by pure parsimony. In Proceedings of the Fourteenth Symposium on Combinatorial Pattern Matching (CPM '03), pages 144-155, 2003.
11. B. V. Halldórsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and S. Istrail. A survey of computational methods for determining haplotypes. In Computational Methods for SNPs and Haplotype Inference (LNCS 2983), pages 26-47, 2004.
12. E. Halperin and E. Eskin. Haplotype reconstruction from genotype data using imperfect phylogeny. Bioinformatics, 20:1842-1849, 2004.
13. 1-∈. Acta Mathematica, 182:105-142, 1999.
14. M. E. Hawley and K. K. Kidd. HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes. Journal of Heredity, 86:409-411, 1995.
15. E. Hubbell. Finding a maximum parsimony solution to haplotype phase is NP-hard. Personal communication.
16. G. Lancia, M. C. Pinotti, and R. Rizzi. Haplotyping populations by pure parsimony. Complexity, exact and approximation algorithms. INFORMS Journal on Computing, 16:348-359, 2004.
17. J. C. Long, R. C. Williams, and M. Urbanek. An E-M algorithm and testing strategy for multiple-locus haplotypes. American Journal of Human Genetics, 56(2):799-810, 1995.
18. T. Niu, Z. S. Qin, X. Xu, and J. S. Liu. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. American Journal of Human Genetics, 70:157-169, 2002.
19. N. Patil et al. Blocks of limited haplotype diversity revealed by high resolution scanning of human chromosome 21. Science, 294:1719-1723, 2001.
20. E. Petrank. The hardness of approximations: gap location. Computational. Complexity, 4:133-157, 1994.
21. M. Stephens, N. J. Smith, and P. Donnelly. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68:978-989, 2001.