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Diploid Alignments and Haplotyping

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Bioinformatics Research and Applications (ISBRA 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9096))

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Abstract

Sequence alignments have been studied for decades under the simplified model of a consensus sequence representing a chromosome. A natural question is if there is some more accurate notion of alignment for diploid (and in general, polyploid) organisms. We have developed such a notion in our recent work, but unfortunately the computational complexity remains open for such a diploid pair-wise alignment; only a trivial exponential algorithm is known that goes over all possible diploid alignments. In this paper, we shed some light on the complexity of diploid alignments by showing that a haplotyping version, involving three diploid inputs, is polynomial time solvable.

Partially supported by Academy of Finland under grant 284598 (CoECGR).

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References

  1. Browning, S.R., Browning, B.L.: Haplotype phasing: existing methods and new developments. Nature Reviews Genetics 12(10), 703–714 (2011)

    Article  Google Scholar 

  2. Chen, W., Li, B., Zeng, Z., Sanna, S., Sidore, C., Busonero, F., Kang, H.M., Li, Y., Abecasis, G.R.: Genotype calling and haplotyping in parent-offspring trios. Genome Research 23(1), 142–151 (2013)

    Article  Google Scholar 

  3. Zhi-Zhong Chen, Fei Deng, and Lusheng Wang. Exact algorithms for haplotype assembly from whole-genome sequence data. Bioinformatics, btt349 (2013)

    Google Scholar 

  4. Durbin, R., Eddy, S.R., Krogh, A., Mitchison, G.: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press (1998)

    Google Scholar 

  5. Gusfield, D.: Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press (1997)

    Google Scholar 

  6. Hirschberg, D.S.: A linear space algorithm for computing maximal common subsequences. Communications of the ACM 18(6), 341–343 (1975)

    Article  MATH  MathSciNet  Google Scholar 

  7. Lee, C., Grasso, C., Sharlow, M.F.: Multiple sequence alignment using partial order graphs. Bioinformatics 18(3), 452–464 (2002)

    Article  Google Scholar 

  8. Löytynoja, A., Vilella, A.J., Goldman, N.: Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics 28(13), 1684–1691 (2012)

    Article  Google Scholar 

  9. Mäkinen, V., Valenzuela, D.: Recombination-aware alignment of diploid individuals. BMC Genomics 15(suppl. 6), S15 (2014)

    Google Scholar 

  10. Marchini, J., Cutler, D., Patterson, N., Stephens, M., Eskin, E., Halperin, E., Lin, S., Qin, Z.S., Munro, H.M., Abecasis, G.R., et al.: A comparison of phasing algorithms for trios and unrelated individuals. The American Journal of Human Genetics 78(3), 437–450 (2006)

    Article  Google Scholar 

  11. Pabinger, S., Dander, A., Fischer, M., Snajder, R., Sperk, M., Efremova, M., Krabichler, B., Speicher, M.R., Zschocke, J., Trajanoski, Z.: A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in Bioinformatics 15(2), 256–278 (2014)

    Article  Google Scholar 

  12. Patterson, M., Marschall, T., Pisanti, N., van Iersel, L., Stougie, L., Klau, G.W., Schönhuth, A.: whatsHap: Haplotype assembly for future-generation sequencing reads. In: Sharan, R. (ed.) RECOMB 2014. LNCS, vol. 8394, pp. 237–249. Springer, Heidelberg (2014)

    Chapter  Google Scholar 

  13. Peters, B.A., Kermani, B.G., Sparks, A.B., Alferov, O., Hong, P., Alexeev, A., Jiang, Y., Dahl, F., Tang, T., Haas, J., et al.: Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 487(7406), 190–195 (2012)

    Article  Google Scholar 

  14. Powell, D.R., Allison, L., Dix, T.I.: A versatile divide and conquer technique for optimal string alignment. Information Processing Letters 70(3), 127–139 (1999)

    Article  MathSciNet  Google Scholar 

  15. Weber, J.L., Wong, C.: Mutation of human short tandem repeats. Human molecular genetics 2(8), 1123–1128 (1993)

    Article  Google Scholar 

  16. Wittler, R.: Unraveling overlapping deletions by agglomerative clustering. BMC Genomics 14(S-1), S12 (2013)

    Google Scholar 

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Correspondence to Veli Mäkinen .

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Mäkinen, V., Valenzuela, D. (2015). Diploid Alignments and Haplotyping. In: Harrison, R., Li, Y., Măndoiu, I. (eds) Bioinformatics Research and Applications. ISBRA 2015. Lecture Notes in Computer Science(), vol 9096. Springer, Cham. https://doi.org/10.1007/978-3-319-19048-8_20

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  • DOI: https://doi.org/10.1007/978-3-319-19048-8_20

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-19047-1

  • Online ISBN: 978-3-319-19048-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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