TY - JOUR
T1 - Islands of tractability for parsimony haplotyping
AU - Sharan, Roded
AU - Halldórsson, Bjarni V.
AU - Istrail, Sorin
PY - 2006/7
Y1 - 2006/7
N2 - 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.
AB - 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.
KW - Analysis of algorithms and problem complexity
KW - Biology and genetics
KW - Graph algorithms
UR - http://www.scopus.com/inward/record.url?scp=33747393333&partnerID=8YFLogxK
U2 - 10.1109/TCBB.2006.40
DO - 10.1109/TCBB.2006.40
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C2 - 17048467
AN - SCOPUS:33747393333
SN - 1545-5963
VL - 3
SP - 303
EP - 311
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics
IS - 3
M1 - 1668028
ER -