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Kirzhner, Valery; Nevo, Eviatar; Korol, Abraham B.; Bolshoy, Alexander

doi:10.1023/a:1024553109779

Cited by 20 publications

(3 citation statements)

References 16 publications

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“…Properties like conserved sequence repeats [58], “periodicity signatures” – the formal representation of periodic sequence patterns related to DNA curvature [59] and compositional spectra based on imperfect occurrences of long olignucleotide words [60, 61] are also potentially characteristic of different ecological groups of microbes. For instance, the archaea of the order Halobacteriaceae displayed the “periodicity signatures” distinct from other archaeal species, which might be due to their early divergence from other archaeal lineages, extensive lateral gene transfer or adaptation to high salt environments [59].…”

Section: Sequence Features Of Microbial Genomes Influenced By Lifestylementioning

confidence: 99%

Microbial Lifestyle and Genome Signatures

Dutta

Paul²

2012

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Microbes are known for their unique ability to adapt to varying lifestyle and environment, even to the extreme or adverse ones. The genomic architecture of a microbe may bear the signatures not only of its phylogenetic position, but also of the kind of lifestyle to which it is adapted. The present review aims to provide an account of the specific genome signatures observed in microbes acclimatized to distinct lifestyles or ecological niches. Niche-specific signatures identified at different levels of microbial genome organization like base composition, GC-skew, purine-pyrimidine ratio, dinucleotide abundance, codon bias, oligonucleotide composition etc. have been discussed. Among the specific cases highlighted in the review are the phenomena of genome shrinkage in obligatory host-restricted microbes, genome expansion in strictly intra-amoebal pathogens, strand-specific codon usage in intracellular species, acquisition of genome islands in pathogenic or symbiotic organisms, discriminatory genomic traits of marine microbes with distinct trophic strategies, and conspicuous sequence features of certain extremophiles like those adapted to high temperature or high salinity.

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Section: Sequence Features Of Microbial Genomes Influenced By Lifestylementioning

confidence: 99%

Microbial Lifestyle and Genome Signatures

Dutta

Paul²

2012

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“…It can be seen that data errors, even as high as in case B, still do not prevent the evaluation of the number of different genomes. It was shown by us earlier [3,25], that a fragment spectrum usually almost coincides with the whole-genome spectrum for a large number of genomes. The exception from this finding is a small number of certain bacteria that have significant differences in the spectra of their genome fragments, namely, Borrelia burgdorferi [3,26], and some Spirochete bacteria.…”

Section: Design Of the Numerical Experimentsmentioning

confidence: 86%

Evaluating the Number of Different Genomes in a Metagenome by Means of the Compositional Spectra Approach

Kirzhner

Toledano-Kitai

Volkovich

2020

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Determination of metagenome composition is still one of the most interesting problems of bioinformatics. It involves a wide range of mathematical methods, from probabilistic models of combinatorics to cluster analysis and pattern recognition techniques. The successful advance of rapid sequencing methods and fast and precise metagenome analysis will increase the diagnostic value of healthy or pathological human metagenomes. The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study. The approach is based on analysis of the compositional spectra of subsequently sequenced samples of the medium. Its essential feature is using random fluctuations in the bacteria number in different samples of the same metagenome. The possibility of effective implementation of the algorithm in the presence of data errors is also discussed. In the work, the algorithm of a metagenome evaluation is described, including the estimation of the genome number and the identification of the genomes with known compositional spectra. It should be emphasized that evaluating the genome number in a metagenome can be always helpful, regardless of the metagenome separation techniques, such as clustering the sequencing results or marker analysis.

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“…[22,31,34,36,38,50], and genome informatics, cf. [4,27,33,41]. Moreover, particle physicists are currently utilizing clustering techniques when the ouput-data of large particle detectors, such as ATLAS, CMS 2 or ALICE, cf.…”

Section: Introductionmentioning

confidence: 99%

Coresets for $(k,l)$-Clustering under the Fréchet Distance

Rohde¹

2019

Preprint

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Clustering is the task of partitioning a given set of geometric objects. This is thoroughly studied when the objects are points in the euclidean space. There are also several approaches for points in general metric spaces. In this thesis we consider clustering polygonal curves, i.e., curves composed of line segments, under the Fréchet distance. We obtain clusterings by minimizing an objective function, which yields a set of centers that induces a partition of the input.The objective functions we consider is the so called (k, l)-Center, where we are to find the k center-curves that minimize the maximum distance between any input-curve and a nearest center-curve and the so called k-Median, where we are to find the k center-curves that minimize the sum of the distances between the input-curves and a nearest center-curve.Given a set of n polygonal curves, we are interested in reducing this set to an ε-coreset, i.e., a notably smaller set of curves that has a very similar clustering-behavior. We develop a construction method for such ε-coresets for the (k, 2)-Center, that yields ε-coresets of size of a polynomial of 1 /ε, in time linear in n and a polynomial of 1 /ε, for line segments. Also, we develop a construction technique for the (k, l)-Center that yields ε-coresets of size exponential in m with basis 1 /ε, in time sub-quadratic in n and exponential in m with basis 1 /ε, for general polygonal curves, if the given curves are of "good" structure.Finally, we develop a construction method for the k-Median, that yields ε-coresets of size polylogarithmic in n and a polynomial of 1 /ε, in time linear in n and a polynomial of 1 /ε. This thesis is dedicated to my mother Antonia and my wife Lia who encouraged (and sometimes pushed) me to live out my curiosity in the scientific disciplines, which lead to this thesis and thus to the completion of my studies, eventually. Also, I want to thank Maike and Hendrik, not only for their good supervision, but also for their general support. Furthermore, I owe them the opportunity to begin my doctoral studies, for which I am very grateful.

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Cited by 20 publications

References 16 publications

Microbial Lifestyle and Genome Signatures

Microbial Lifestyle and Genome Signatures

Evaluating the Number of Different Genomes in a Metagenome by Means of the Compositional Spectra Approach

Coresets for $(k,l)$-Clustering under the Fréchet Distance

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