Skip to main content
SpringerLink
Log in
SpringerLink
Log in

Discovering Kinship through Small Subsets

  • Conference paper
Algorithms in Bioinformatics (WABI 2010)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6293))

Included in the following conference series:

Abstract

In kinship inference, we identify genealogical relationships among organisms. One such problem is sibgroup reconstruction: given a population of same-generation individuals, partition it into sibgroups resulting from mating events. Minimizing the number of matings is NP-hard to approximate, yet a simple heuristic, based on identifying population triplets that can be from the same sibgroup, performs comparably to better than integer programming algorithms in a fraction of the running time. With high probability if we study many loci in the genome, and large populations, our polynomial-time heuristic finds the true sibgroups, assuming a standard probabilistic inheritance model.

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

Access this chapter

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 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
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

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Ashley, M., Berger-Wolf, T., Berman, P., Chaovalitwongse, W., DasGupta, B., Kao, M.Y.: On approximating four covering and packing problems. J. Comp. and Sys. Sci. 75(5), 287–302 (2009)

    Article  Google Scholar 

  2. Ashley, M.V., Caballero, I.C., Chaovalitwongse, W., DasGupta, B., Govindan, P., Sheikh, S., Berger-Wolf, T.Y.: Kinalyzer, a computer program for reconstructing sibling groups. Mol. Ecol. Res. 9, 1127–1131 (2009)

    Article  CAS  Google Scholar 

  3. Wilson, A., Barker, J.: Isolation and characterization of 20 polymorphic microsatellite loci for Scaptodrosophila hibisci. Mol. Ecol. Notes 2, 242–244 (2002)

    Google Scholar 

  4. Berger-Wolf, T., Sheikh, S., DasGupta, B., Ashley, M., Caballero, I., Chaovalitwongse, W., Putrevu, S.L.: Reconstructing sibling relationships in wild populations. Bioinf. 23(13); Proceedings of ISMB 2007 (2007)

    Google Scholar 

  5. Chaovalitwongse, W., Chou, C., Berger-Wolf, T., DasGupta, B., Sheikh, S., Ashley, M.V., Caballero, I.C.: New optimization model and algorithm for sibling reconstruction from genetic markers. INFORMS J. Comp. 22(1), 180–194 (2010)

    Article  Google Scholar 

  6. Conner, J.K.: Personal Communication (2006)

    Google Scholar 

  7. Crim, J., Spotila, L., Spotila, J., O’Connor, M., Reina, R., Williams, C., Paladino, F.: The leatherback turtle, Dermochelys coriacea. Mol. Ecol. 11(10), 2097–2106 (2002)

    Article  CAS  PubMed  Google Scholar 

  8. Devdatt, D., Panconesci, A.: Concentration of measure for the analysis of randomized algorithms. Cambridge Press, New York (2009)

    Google Scholar 

  9. Gusfield, D.: Partition-distance: A problem and class of perfect graphs arising in clustering. Info. Proc. Lett. 82(3), 159–164 (2002)

    Article  Google Scholar 

  10. Hammond, R.L., Bourke, A.F.G., Bruford, M.W.: Mating frequency and mating system of the polygynous ant, Leptothorax acervorum. Mol. Ecol. 10(11), 2719–2728 (1999)

    Article  Google Scholar 

  11. Herbinger, C.M., O’Reilly, P.T., Doyle, R.W., Wright, J.M., O’Flynn, F.: Early growth performance of atlantic salmon full-sib families reared in single family tanks versus in mixed family tanks. Aquaculture 173(1-4), 105–116 (1999)

    Article  Google Scholar 

  12. Jerry, D., Evans, B., Kenway, M., Wilson, K.: Development of a microsatellite DNA parentage marker suite for black tiger shrimp Penaeus monodon. Aquaculture, 542–547 (2006)

    Google Scholar 

  13. Sheikh, S., Berger-Wolf, T., Khokhar, A., DasGupta, B.: Consensus methods for reconstruction of sibling relationships from genetic data. In: Proceedings of the 4th Workshop on Advances in Preference Handling (2008)

    Google Scholar 

  14. Sheikh, S., Berger-Wolf, T., Khokhar, A., Caballero, I., Ashley, M., Chaovalitwongse, W., DasGupta, B.: Parsimony-based reconstruction of half-sibling groups. J. Bioinf. and Comp. Biol. (to appear)

    Google Scholar 

  15. Wang, J.: Sibship reconstruction from genetic data with typing errors. Genetics 166, 1968–1979 (2004)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, N2L 3G1, Canada

    Daniel G. Brown

  2. Department of Computer Science, University of Illinois at Chicago, Chicago, IL, 60607, USA

    Tanya Berger-Wolf

Authors
  1. Daniel G. Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tanya Berger-Wolf
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. School of Computing Sciences, University of East Anglia, NR 7TJ, Norwich, UK

    Vincent Moulton

  2. Lewis-Sigler Institute for Integrative Genomics, Department of Computer Science, Princeton University, NJ 08544, Princeton, USA

    Mona Singh

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Brown, D.G., Berger-Wolf, T. (2010). Discovering Kinship through Small Subsets. In: Moulton, V., Singh, M. (eds) Algorithms in Bioinformatics. WABI 2010. Lecture Notes in Computer Science(), vol 6293. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15294-8_10

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-15294-8_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-15293-1

  • Online ISBN: 978-3-642-15294-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation