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

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...

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Hauptverfasser:	Panconesi, Alessandro, Sozio, Mauro
Format:	Tagungsbericht
Sprache:	eng
Schlagworte:	Algorithmics. Computability. Computer arithmetics Applied sciences Biological and medical sciences Computer science control theory systems Dynamic Programming Algorithm Exact sciences and technology Fast Heuristic Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Null Entry Output Matrix Reading Error Theoretical computing
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Beschreibung
Zusammenfassung:	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.
ISSN:	0302-9743 1611-3349
DOI:	10.1007/978-3-540-30219-3_23