Skip to main content
SpringerLink
Log in
Book cover

International Symposium on Bioinformatics Research and Applications

ISBRA 2015: Bioinformatics Research and Applications pp 235–246Cite as

Diploid Alignments and Haplotyping

  • Conference paper

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

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).

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

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 

Download references

Author information

Authors and Affiliations

  1. Helsinki Institute for Information Technology HIIT , Department of Computer Science, University of Helsinki, Helsinki, Finland

    Veli Mäkinen & Daniel Valenzuela

Authors
  1. Veli Mäkinen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Daniel Valenzuela
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Veli Mäkinen .

Editor information

Editors and Affiliations

  1. Georgia State University, Atlanta, USA

    Robert Harrison

  2. Old Dominion University, Norfolk, USA

    Yaohang Li

  3. University of Connecticut, Storrs, Connecticut, USA

    Ion Măndoiu

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this paper

Cite this paper

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

Download citation

  • 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)

Publish with us

Policies and ethics

Search

Navigation