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Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction

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Algorithms in Bioinformatics (WABI 2004)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3240))

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Abstract

We study the single individual SNP haplotype reconstruction problem. We introduce a simple heuristic and prove experimentally that is very fast and accurate. In particular, when compared with a dynamic programming of [8] it is much faster and also more accurate. We expect Fast Hare to be very useful in practical applications. We also introduce a combinatorial problem related to the SNP haplotype reconstruction problem that we call Min Element Removal. We prove its NP-hardness in the gapless case and its O(log n)-approximability in the general case.

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References

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Author information

Authors and Affiliations

  1. Informatica, La Sapienza, via Salaria 113, 00198, Roma, Italy

    Alessandro Panconesi & Mauro Sozio

Authors
  1. Alessandro Panconesi
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  2. Mauro Sozio
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Editor information

Editors and Affiliations

  1. Department of Informatics and Computational Biology Unit, HIB, University of Bergen, 5020, Bergen, Norway

    Inge Jonassen

  2. Department of Biology,, Penn Center for Bioinformatics, Penn Genomics Institute, 415 S. University Ave., PA 19104, Philadelphia, USA

    Junhyong Kim

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© 2004 Springer-Verlag Berlin Heidelberg

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Panconesi, A., Sozio, M. (2004). Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction. In: Jonassen, I., Kim, J. (eds) Algorithms in Bioinformatics. WABI 2004. Lecture Notes in Computer Science(), vol 3240. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30219-3_23

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  • DOI: https://doi.org/10.1007/978-3-540-30219-3_23

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-23018-2

  • Online ISBN: 978-3-540-30219-3

  • eBook Packages: Springer Book Archive

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