Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments

El-Mabrouk, Nadia

doi:10.1007/3-540-45123-4_20

Cited by 83 publications

(71 citation statements)

References 8 publications

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“…For unequal genomes with gene insertions/deletions, El-Marbrouk [2] proposed a definition of the distance between such genomes based on the assumption that the cost of deleting one continuous block of genes is equal to that of one inversion operation. This implies that deleting blocks with more genes is always preferred.…”

Section: B Distance Computationmentioning

confidence: 99%

Phylogenetic reconstruction with gene rearrangements and gene losses

Zhang

Tang

2010

2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

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Abstract-Reconstructing phylogenies from gene-order data has become very attractive in the research of evolution these years. So far, most methods can only treat genomes with equal gene contents with each gene appearing exactly once in each genome. In this paper, we propose a new distance measurement for genomes with inversions and insertions/deletions that comply with triangle inequality. Based on this distance, we develop a new method to solve the median problem of unequal gene content, which are used to reconstruct both phylogenies and ancestral genomes. We test our method on simulated datasets under various conditions and the experimental results show that our distance measurement can produce more accurate phylogenetic trees compared with other popular methods for unequal genomes. Also our median algorithm produces remarkably more accurate ancestral genomes than the only unequal genome median solver that is currently available.

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Section: B Distance Computationmentioning

confidence: 99%

Phylogenetic reconstruction with gene rearrangements and gene losses

Zhang

Tang

2010

2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

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“…(In absence of this constraint, of course, the most parsimonious edit sequence is almost always that which deletes the entire genome G 1 as a single operation, then insert the entire genome G 2 , an absurd scenario.) Once that identification has been made, the algorithms of ElMabrouk [9] and of our group [8,12,17,18] can complete the work of finding one ore more parsimonious edit sequences.…”

Section: Preliminariesmentioning

confidence: 99%

A Framework for Orthology Assignment from Gene Rearrangement Data

Swenson

Pattengale

Moret

2005

Comparative Genomics

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Abstract. Gene rearrangements have successfully been used in phylogenetic reconstruction and comparative genomics, but usually under the assumption that all genomes have the same gene content and that no gene is duplicated. While these assumptions allow one to work with organellar genomes, they are too restrictive when comparing nuclear genomes. The main challenge is how to deal with gene families, specifically, how to identify orthologs. While searching for orthologies is a common task in computational biology, it is usually done using sequence data. We approach that problem using gene rearrangement data, provide an optimization framework in which to phrase the problem, and present some preliminary theoretical results.

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“…The algorithmic problems concerning cycle packings are typically hard ( [5], [11], [20]) and approximation algorithms are described ( [11], [17]). Several authors mention practical applications in computational biology ( [3], [8], [13]) or the design of optical networks ( [1]). In this paper, we investigate maximum cycle packings in polyhedral graphs G. We derive different bounds on the cardinality of such packings depending on the size of G, the order of G and the number of faces of G, respectively.…”

Section: Introductionmentioning

confidence: 99%