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Volumn 4645 LNBI, Issue , 2007, Pages 49-60

A fast and accurate heuristic for the single individual SNP haplotyping problem with many gaps, high reading error rate and low coverage

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOMES; DNA SEQUENCES; HEURISTIC METHODS; MEDICINE; MOLECULAR BIOLOGY; POLYMORPHISM; POLYNOMIALS;

EID: 37249002274     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-74126-8_6     Document Type: Conference Paper
Times cited : (9)

References (16)
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    • Bafna, V., Istrail, S., Lancia, G., Rizzi, R.: Polynomial and APX-hard cases of the individual haplotyping problem. Theor. Comput. Sci. 335(1), 109-125 (2005)
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    • Bafna, V.1    Istrail, S.2    Lancia, G.3    Rizzi, R.4
  • 2
    • 0348226177 scopus 로고    scopus 로고
    • The haplotyping problem: An overview of computational models and solutions
    • Bonizzoni, P., Della Vedova, G., Dondi, R., Li, J.: The haplotyping problem: an overview of computational models and solutions. J. Comput. Sci. Technol. 18(6), 675-688 (2003)
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  • 3
    • 33646192744 scopus 로고    scopus 로고
    • Cilibrasi, R., van Iersel, L., Kelk, S., Tromp, J.: On the complexity of several haplotyping problems. In: Casadio, R., Myers, G. (eds.) WABI 2005. LNCS (LNBI), 3692, pp. 128-139. Springer, Heidelberg (2005)
    • Cilibrasi, R., van Iersel, L., Kelk, S., Tromp, J.: On the complexity of several haplotyping problems. In: Casadio, R., Myers, G. (eds.) WABI 2005. LNCS (LNBI), vol. 3692, pp. 128-139. Springer, Heidelberg (2005)
  • 4
    • 36549019057 scopus 로고    scopus 로고
    • Cilibrasi, R., van Iersel, L., Kelk, S., Tromp, J.: On the complexity of the single individual SNP haplotyping problem. Algorithmica (in print, 2007)
    • Cilibrasi, R., van Iersel, L., Kelk, S., Tromp, J.: On the complexity of the single individual SNP haplotyping problem. Algorithmica (in print, 2007)
  • 5
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    • A haplotype map of the human genome
    • The International HapMap Consortium
    • The International HapMap Consortium: A haplotype map of the human genome. Nature 437, 1299-1320 (2005), http://snp.cshl.org
    • (2005) Nature , vol.437 , pp. 1299-1320
  • 6
    • 33750258418 scopus 로고    scopus 로고
    • Haplotype Inference
    • ch. 1, pp, CRC Press, Boca Raton, USA
    • Gusfield, D., Orzack, S.H.: Haplotype Inference. In: CRC Handbook on Bioinformatics, ch. 1, pp. 1-25. CRC Press, Boca Raton, USA (2005)
    • (2005) CRC Handbook on Bioinformatics , pp. 1-25
    • Gusfield, D.1    Orzack, S.H.2
  • 7
    • 84943255398 scopus 로고    scopus 로고
    • Lancia, G., Bafna, V., Istrail, S., Lippert, R., Schwartz, R.: SNPs problems, complexity, and algorithms. In: Meyer auf der Heide, F. (ed.) ESA 2001. LNCS, 2161, pp. 182-193. Springer, Heidelberg (2001)
    • Lancia, G., Bafna, V., Istrail, S., Lippert, R., Schwartz, R.: SNPs problems, complexity, and algorithms. In: Meyer auf der Heide, F. (ed.) ESA 2001. LNCS, vol. 2161, pp. 182-193. Springer, Heidelberg (2001)
  • 11
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    • Panconesi, A., Sozio, M.: Fast hare: A fast heuristic for single individual SNP haplotype reconstruction. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), 3240, pp. 266-277. Springer, Heidelberg (2004)
    • Panconesi, A., Sozio, M.: Fast hare: A fast heuristic for single individual SNP haplotype reconstruction. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 266-277. Springer, Heidelberg (2004)
  • 12
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    • Sachidanandam, R., et al.: A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928-933 (2001)
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  • 13
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    • Rizzi, R., Bafna, V., Istrail, S., Lancia, G.: Practical algorithms and fixedparameter treatability for the single individual SNP haplotyping problem. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, 2452, pp. 29-43. Springer, Heidelberg (2002)
    • Rizzi, R., Bafna, V., Istrail, S., Lancia, G.: Practical algorithms and fixedparameter treatability for the single individual SNP haplotyping problem. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 29-43. Springer, Heidelberg (2002)
  • 14
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    • Wang, R.-S., Wu, L.-Y., Li, Z.-P., Zhang, X.-S.: Haplotype reconstruction from SNP fragments by minimum error correction. Bioinformatics 21(10), 2456-2462 (2005)
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2456-2462
    • Wang, R.-S.1    Wu, L.-Y.2    Li, Z.-P.3    Zhang, X.-S.4
  • 15
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