Algorithms for reconstruction of chromosomal structures

Background One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree generation. Such objects can include nucleotide and amino acid sequences, chrom...

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Veröffentlicht in:	BMC bioinformatics Jg. 17; H. 1; S. 40
Hauptverfasser:	Lyubetsky, Vassily, Gershgorin, Roman, Seliverstov, Alexander, Gorbunov, Konstantin
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	London BioMed Central 19.01.2016
Schlagworte:	Algorithms Bioinformatics Biomedical and Life Sciences Chromosome Structures - chemistry Comparative genomics Computational Biology - methods Computational Biology/Bioinformatics Computer Appl. in Life Sciences Computer Simulation Life Sciences Microarrays Models, Molecular Phylogeny Research Article Software Lowest weight transformation of one chromosome structure into another Generation of a phylogenetic tree of chromosomal structures Rearrangement of chromosomal structure Ancestral chromosomal structure Distance between chromosomal structures Exact linear algorithm calculating the distance and transformation Exact reconstruction algorithm with cubic complexity Chromosomal structure
ISSN:	1471-2105, 1471-2105
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Abstract	Background One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree generation. Such objects can include nucleotide and amino acid sequences, chromosomal structures, etc. The structures can have any set of linear and circular chromosomes, variable gene composition and include any number of paralogs, as well as any weights of individual evolutionary operations to transform a chromosome structure. Many heuristic algorithms were proposed for this purpose, but there are just a few exact algorithms with low (linear, cubic or similar) polynomial computational complexity among them to our knowledge. The algorithms naturally start from the calculation of both the distance between two structures and the shortest sequence of operations transforming one structure into another. Such calculation per se is an NP-hard problem. Results A general model of chromosomal structure rearrangements is considered. Exact algorithms with almost linear or cubic polynomial complexities have been developed to solve the problems for the case of any chromosomal structure but with certain limitations on operation weights. The computer programs are tested on biological data for the problem of mitochondrial or plastid chromosomal structure reconstruction. To our knowledge, no computer programs are available for this model. Conclusions Exactness of the proposed algorithms and such low polynomial complexities were proved. The reconstructed evolutionary trees of mitochondrial and plastid chromosomal structures as well as the ancestral states of the structures appear to be reasonable.
AbstractList	One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree generation. Such objects can include nucleotide and amino acid sequences, chromosomal structures, etc. The structures can have any set of linear and circular chromosomes, variable gene composition and include any number of paralogs, as well as any weights of individual evolutionary operations to transform a chromosome structure. Many heuristic algorithms were proposed for this purpose, but there are just a few exact algorithms with low (linear, cubic or similar) polynomial computational complexity among them to our knowledge. The algorithms naturally start from the calculation of both the distance between two structures and the shortest sequence of operations transforming one structure into another. Such calculation per se is an NP-hard problem.BACKGROUNDOne of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree generation. Such objects can include nucleotide and amino acid sequences, chromosomal structures, etc. The structures can have any set of linear and circular chromosomes, variable gene composition and include any number of paralogs, as well as any weights of individual evolutionary operations to transform a chromosome structure. Many heuristic algorithms were proposed for this purpose, but there are just a few exact algorithms with low (linear, cubic or similar) polynomial computational complexity among them to our knowledge. The algorithms naturally start from the calculation of both the distance between two structures and the shortest sequence of operations transforming one structure into another. Such calculation per se is an NP-hard problem.A general model of chromosomal structure rearrangements is considered. Exact algorithms with almost linear or cubic polynomial complexities have been developed to solve the problems for the case of any chromosomal structure but with certain limitations on operation weights. The computer programs are tested on biological data for the problem of mitochondrial or plastid chromosomal structure reconstruction. To our knowledge, no computer programs are available for this model.RESULTSA general model of chromosomal structure rearrangements is considered. Exact algorithms with almost linear or cubic polynomial complexities have been developed to solve the problems for the case of any chromosomal structure but with certain limitations on operation weights. The computer programs are tested on biological data for the problem of mitochondrial or plastid chromosomal structure reconstruction. To our knowledge, no computer programs are available for this model.Exactness of the proposed algorithms and such low polynomial complexities were proved. The reconstructed evolutionary trees of mitochondrial and plastid chromosomal structures as well as the ancestral states of the structures appear to be reasonable.CONCLUSIONSExactness of the proposed algorithms and such low polynomial complexities were proved. The reconstructed evolutionary trees of mitochondrial and plastid chromosomal structures as well as the ancestral states of the structures appear to be reasonable. One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree generation. Such objects can include nucleotide and amino acid sequences, chromosomal structures, etc. The structures can have any set of linear and circular chromosomes, variable gene composition and include any number of paralogs, as well as any weights of individual evolutionary operations to transform a chromosome structure. Many heuristic algorithms were proposed for this purpose, but there are just a few exact algorithms with low (linear, cubic or similar) polynomial computational complexity among them to our knowledge. The algorithms naturally start from the calculation of both the distance between two structures and the shortest sequence of operations transforming one structure into another. Such calculation per se is an NP-hard problem. A general model of chromosomal structure rearrangements is considered. Exact algorithms with almost linear or cubic polynomial complexities have been developed to solve the problems for the case of any chromosomal structure but with certain limitations on operation weights. The computer programs are tested on biological data for the problem of mitochondrial or plastid chromosomal structure reconstruction. To our knowledge, no computer programs are available for this model. Exactness of the proposed algorithms and such low polynomial complexities were proved. The reconstructed evolutionary trees of mitochondrial and plastid chromosomal structures as well as the ancestral states of the structures appear to be reasonable. Background One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree generation. Such objects can include nucleotide and amino acid sequences, chromosomal structures, etc. The structures can have any set of linear and circular chromosomes, variable gene composition and include any number of paralogs, as well as any weights of individual evolutionary operations to transform a chromosome structure. Many heuristic algorithms were proposed for this purpose, but there are just a few exact algorithms with low (linear, cubic or similar) polynomial computational complexity among them to our knowledge. The algorithms naturally start from the calculation of both the distance between two structures and the shortest sequence of operations transforming one structure into another. Such calculation per se is an NP-hard problem. Results A general model of chromosomal structure rearrangements is considered. Exact algorithms with almost linear or cubic polynomial complexities have been developed to solve the problems for the case of any chromosomal structure but with certain limitations on operation weights. The computer programs are tested on biological data for the problem of mitochondrial or plastid chromosomal structure reconstruction. To our knowledge, no computer programs are available for this model. Conclusions Exactness of the proposed algorithms and such low polynomial complexities were proved. The reconstructed evolutionary trees of mitochondrial and plastid chromosomal structures as well as the ancestral states of the structures appear to be reasonable.
ArticleNumber	40
Author	Seliverstov, Alexander Lyubetsky, Vassily Gershgorin, Roman Gorbunov, Konstantin
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Keywords	Lowest weight transformation of one chromosome structure into another Generation of a phylogenetic tree of chromosomal structures Rearrangement of chromosomal structure Ancestral chromosomal structure Distance between chromosomal structures Exact linear algorithm calculating the distance and transformation Exact reconstruction algorithm with cubic complexity Chromosomal structure
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Snippet	Background One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the... One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified...
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SubjectTerms	Algorithms Bioinformatics Biomedical and Life Sciences Chromosome Structures - chemistry Comparative genomics Computational Biology - methods Computational Biology/Bioinformatics Computer Appl. in Life Sciences Computer Simulation Life Sciences Microarrays Models, Molecular Phylogeny Research Article Software
Title	Algorithms for reconstruction of chromosomal structures
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