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

  • Alessandro Panconesi
  • Mauro Sozio
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3240)


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.


Dynamic Programming Algorithm Output Matrix Reading Error Fast Heuristic Null Entry 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Alessandro Panconesi
    • 1
  • Mauro Sozio
    • 1
  1. 1.Informatica, La SapienzaRomaItaly

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