An improved (and practical) parameterized algorithm for the individual haplotyping problem MFR with mate-pairs

Algorithmica (New York)

Volumn 52, Issue 2, 2008, Pages 250-266

  Xie, Minzhu ^a,b   Wang, Jianxin ^a  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b HUNAN NORMAL UNIVERSITY   (China)

Author keywords

Genotype; Haplotype; NP hardness; Parameterized algorithm; SNP (single nucleotide polymorphism)

Indexed keywords

COMPUTATIONAL PROBLEMS; GENOTYPE; HAPLOTYPE; HAPLOTYPES; HAPLOTYPING; NP-HARDNESS; PARAMETERIZED; PARAMETERIZED ALGORITHM; SNP (SINGLE-NUCLEOTIDE POLYMORPHISM);

ORGANIC ACIDS;

NUCLEIC ACIDS;

EID: 50849099541     PISSN: 01784617     EISSN: 14320541     Source Type: Journal    
DOI: 10.1007/s00453-007-9150-2     Document Type: Article

References (18)

1. Venter, J.C., Adams, M.D., Myers, E.W., et al.: The sequence of the Human Genome. Science 291, 1304-1351 (2001)
2. The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320 (2005)
3. Gabriel, S.B., Schaffner, S.F., Nguyen, H., et al.: The structure of haplotype blocks in the Human Genome. Science 296, 2225-2229 (2002)
4. Stephens, J.C., Schneider, J.A., Tanguay, D.A., et al.: Haplotype variation and linkage disequilibrium in 313 human genes. Science 293, 489-493 (2001)
5. Horikawa, Y., Oda, N., Cox, N.J., et al.: Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat. Genet. 26, 163-175 (2000)
6. Lancia, G., Bafna, V., Istrail, S., Lippert, R., Schwartz, R.: SNPs problems, complexity and algorithms. In: Proc. ESA, pp. 182-193 (2001)
7. Bafna, V., Istrail, S., Lancia, G., Rizzi, R.: Polynomial and APX-hard cases of the individual haplotyping problem. Theor. Comput. Sci. 335, 109-125 (2005)
8. Roach, J.C., Wang, K., Hood, L.: Pairwise end sequencing: A unified approach to genomic mapping and sequencing. Genomics 26(2), 345-353 (1995)
9. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001)
10. The International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928-933 (2001)
11. Hinds, D.A., Stuve, L.L., Nilsen, G.B., et al.: Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072-1079 (2005)
12. Sanger, F., Nicklen, S., Coulson, A.R.: DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. 74(12), 5463-5467 (1977)
13. Huson, D.H., Halpern, A.L., Lai, Z., Myers, E.W., Reinert, K., Sutton, G.G.: Comparing assemblies using fragments and mate-pairs. In: Proc. WABI. Lecture Notes in Computer Science, vol. 2149, pp. 294-306. Springer, New York (2001)
14. Li, L., Khuri, S.: A comparison of DNA fragment assembly algorithms. In: Proc. METMBS, pp. 329-335 (2004)
15. Wernicke, S.: On the algorithmic tractability of single nucleotide polymorphism (SNP) analysis and related problems. Ph. D. thesis, University of Tübingen, 2003
16. Panconesi, A., Sozio, M.: Fast hare: A fast heuristic for single individual SNP haplotype reconstruction. In: Proc. WABI. Lecture Notes in Computer Science, vol. 3240, pp. 266-277. Springer, New York (2004)
17. Hüffner, F.: Algorithm engineering for optimal graph bipartization. In: Proc. WEA. Lecture Notes in Computer Science, vol. 3503, pp. 240-252. Springer, New York (2005)
18. Myers, G.: A dataset generator for whole genome shotgun sequencing. In: Proc. ISMB, pp. 202-210 (1999)