Islands of tractability for parsimony haplotyping

Roded Sharan; Bjarni V. Halldórsson; Sorin Istrail

doi:10.1109/CSB.2005.37

Islands of tractability for parsimony haplotyping

Roded Sharan, Bjarni V. Halldórsson, Sorin Istrail

School of Computer Sciences

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

We study the parsimony approach to haplotype inference, which calls for finding a set of haplotypes of minimum cardinality that explains an input set of genotypes. We prove that the problem is APX-hard even in very restricted cases. On the positive side, we identify islands of tractability for the problem, by focusing on instances with specific structure of haplotype sharing among the input genotypes. We exploit the structure of those instance to give polynomial and constant-approximation algorithms to the problem. We also show that the general parsimony haplotyping problem is fixed parameter tractable.

Original language	English
Title of host publication	Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005
Pages	65-72
Number of pages	8
DOIs	https://doi.org/10.1109/CSB.2005.37
State	Published - 2005
Event	2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005 - Stanford, CA, United States Duration: 8 Aug 2005 → 11 Aug 2005

Publication series

Name	Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005
Volume	2005

Conference

Conference	2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005
Country/Territory	United States
City	Stanford, CA
Period	8/08/05 → 11/08/05

Keywords

Approximation algorithm
Complexity
Fixed parameter tractability
Genotype
Haplotype inference
Parsimony

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10.1109/CSB.2005.37

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title = "Islands of tractability for parsimony haplotyping",

abstract = "We study the parsimony approach to haplotype inference, which calls for finding a set of haplotypes of minimum cardinality that explains an input set of genotypes. We prove that the problem is APX-hard even in very restricted cases. On the positive side, we identify islands of tractability for the problem, by focusing on instances with specific structure of haplotype sharing among the input genotypes. We exploit the structure of those instance to give polynomial and constant-approximation algorithms to the problem. We also show that the general parsimony haplotyping problem is fixed parameter tractable.",

keywords = "Approximation algorithm, Complexity, Fixed parameter tractability, Genotype, Haplotype inference, Parsimony",

author = "Roded Sharan and Halld{\'o}rsson, {Bjarni V.} and Sorin Istrail",

year = "2005",

doi = "10.1109/CSB.2005.37",

language = "אנגלית",

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series = "Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005",

pages = "65--72",

booktitle = "Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005",

note = "null ; Conference date: 08-08-2005 Through 11-08-2005",

}

Sharan, R, Halldórsson, BV & Istrail, S 2005, Islands of tractability for parsimony haplotyping. in Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005., 1498007, Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005, vol. 2005, pp. 65-72, 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005, Stanford, CA, United States, 8/08/05. https://doi.org/10.1109/CSB.2005.37

Islands of tractability for parsimony haplotyping. / Sharan, Roded; Halldórsson, Bjarni V.; Istrail, Sorin.

Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005. 2005. p. 65-72 1498007 (Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005; Vol. 2005).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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KW - Complexity

KW - Fixed parameter tractability

KW - Genotype

KW - Haplotype inference

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ER -

Islands of tractability for parsimony haplotyping

Abstract

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Conference

Keywords

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