NDLI: Mixed and Circular Multichromosomal Genomic Median Problem

Content Provider	Society for Industrial and Applied Mathematics (SIAM)
Author	Haghighi, Maryam Boyd, Sylvia
Copyright Year	2013
Abstract	We study the problem of finding the breakpoint median for multichromosomal unsigned genomes that contain circular or mixed (circular and linear) chromosomes. It has been shown by Tannier, Zheng, and Sankoff that for signed multichromosomal circular or mixed genomes the breakpoint median can be found in polynomial time; however, the complexity of the unsigned versions of the problems were unknown. In this paper, we show that these problems can all be solved in polynomial time. We also study restricted versions of the multichromosomal breakpoint median problem where the number of chromosomes of the median must be a certain number. We show that as soon as we impose a fixed number of chromosomes the problem becomes NP-hard. Moreover, we introduce the notion of partially signed circular or mixed genomes, where both signed and unsigned genes may exist in the same genome. We provide the first study of this form of these breakpoint median problems and show that these problem can also be solved in polynomial time by providing a novel transformation to b-matchings.
Starting Page	63
Ending Page	74
Page Count	12
File Format	PDF
ISSN	08954801
DOI	10.1137/120866439
e-ISSN	10957146
Journal	SIAM Journal on Discrete Mathematics (SJDMEC)
Issue Number	1
Volume Number	27
Language	English
Publisher	Society for Industrial and Applied Mathematics
Publisher Date	2013-01-15
Access Restriction	Subscribed
Subject Keyword	genomic median problem Factorization, matching, partitioning, covering and packing perfect b-matchings breakpoint median problem Graph theory
Content Type	Text
Resource Type	Article
Subject	Mathematics

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