Fast hare: A fast heuristic for single individual SNP haplotype reconstruction

Alessandro Panconesi, Mauro Sozio

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

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.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
EditorsInge Jonassen, Junhyong Kim
PublisherSpringer Verlag
Pages266-277
Number of pages12
ISBN (Print)3540230181, 9783540230182
DOIs
Publication statusPublished - 1 Jan 2004
Externally publishedYes

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3240
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

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