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Consistency of Sequence-Based Gene Clusters

Authors: Wittler, Roland; Maňuch, Ján; Patterson, Murray; Stoye, Jens;

Consistency of Sequence-Based Gene Clusters

Abstract

In comparative genomics, differences or similarities of gene orders are determined to predict functional relations of genes or phylogenetic relations of genomes. For this purpose, various combinatorial models can be used to specify gene clusters--groups of genes that are co-located in a set of genomes. Several approaches have been proposed to reconstruct putative ancestral gene clusters based on the gene order of contemporary species. One prevalent and natural reconstruction criterion is consistency: For a set of reconstructed gene clusters, there should exist a gene order that comprises all given clusters. For permutation-based gene cluster models, efficient methods exist to verify this condition. In this article, we discuss the consistency problem for different gene cluster models on sequences with restricted gene multiplicities. Our results range from linear-time algorithms for the simple model of adjacencies to NP-completeness proofs for more complex models like common intervals.

Keywords

Evolution, Molecular, Base Sequence, Models, Genetic, Multigene Family, Computer Simulation, Sequence Analysis, DNA, Algorithms, Ancestral reconstruction; gene cluster; gene order; whole-genome comparison; Algorithms; Base Sequence; Computer Simulation; Evolution, Molecular; Sequence Analysis, DNA; Models, Genetic; Multigene Family; Modeling and Simulation; Molecular Biology; Genetics; Computational Mathematics; Computational Theory and Mathematics

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
10
Average
Top 10%
Top 10%
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