Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima.

No abstract is available for this paper.

• Publication year

  2000

• Venue

  Nucleic Acids Research

• Publication date

  2000-02-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1093/NAR/28.3.706PMID 10637321PMCID PMC102551
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding

  1999cited by this paper
• Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

  1999cited by this paper
• Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry?

  1999cited by this paper
• Three views of microbial genomes.

  1999cited by this paper
• Is There a Phylogenetic Signal in Prokaryote Proteins?

  1999cited by this paper
• The complete genome of the hyperthermophilic bacterium Aquifex aeolicus

  1998cited by this paper
• Sequence periodicity in complete genomes of archaea suggests positive supercoiling.

  1998cited by this paper
• DNA sequence-dependent deformability deduced from protein-DNA crystal complexes.

  1998cited by this paper
• Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles.

  1998cited by this paper
• Crystal structure of the nucleosome core particle at 2.8 Å resolution

  1997cited by this paper
• Archaeal nucleosomes.

  1997cited by this paper
• Archaeal chromatin: virtual or real?

  1997cited by this paper
• Both DNA gyrase and reverse gyrase are present in the hyperthermophilic bacterium Thermotoga maritima.

  1997cited by this paper
• Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA.

  1996cited by this paper
• Short-range order in two eukaryotic genomes: relation to chromosome structure.

  1996cited by this paper
• The unique DNA topology and DNA topoisomerases of hyperthermophilic archaea.

  1996cited by this paper
• B-DNA twisting correlates with base-pair morphology.

  1995cited by this paper
• Nucleoid proteins.

  1995cited by this paper
• Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria

  1994cited by this paper
• An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking

  1978cited by this paper

• Current Methods for Recombination Detection in Bacteria

  2022cites this paper
• Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information

  2020influential citation
• Evolution of the Stator Elements of Rotary Prokaryote Motors

  2019cites this paper
• Multilayer Perceptron and Evolutionary Radial Basis Function Neural Network Models for Discrimination of HIV-1 Genomes

  2018cites this paper
• Lineage‐associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish‐based LAUPs analysis application (JBLA)

  2018cites this paper
• Application of gene sequences in plant phylogenetic inferences

  2018cites this paper
• Genetic approaches in research on the role of trehalose in plants

  2017cites this paper
• Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction.

  2017cites this paper
• Inferring Orthologs: Open Questions and Perspectives

  2016cites this paper
• Inferring Orthologs: Open Questions and Perspectives

  2016cites this paper
• Short Branch Attraction, the Fundamental Bipartition in Cellular Life, and Eukaryogenesis

  2016cites this paper
• Metabolic and taxonomic diversification in continental magmatic hydrothermal systems 4 . 1

  2015cites this paper
• Correction: Site-Directed Mutagenesis of a Hyperthermophilic Endoglucanase Cel12B from Thermotoga maritima Based on Rational Design

  2015cites this paper
• Inferring Horizontal Gene Transfer

  2015influential citation
• Site-Directed Mutagenesis of a Hyperthermophilic Endoglucanase Cel12B from Thermotoga maritima Based on Rational Design

  2015cites this paper
• Amino acid transport in thermophiles : characterization of an arginine-binding protein in Thermotoga maritima w

  2015cites this paper
• Chemosynthetic carbon metabolism in thermophiles

  2015cites this paper
• The structural code of cyanobacterial genomes

  2014cites this paper
• Otimização de periodicidades fracas em genomas utilizando transformadas de Fourier e algoritmos genéticos.

  2013cites this paper
• Of Trees and Bushes: Phylogenetic Networks as Tools to Detect, Visualize and Model Reticulate Evolution

  2013cites this paper
• Produzione di bioidrogeno in dark fermentation da scarti dell'industria agroalimentale mediante l'impiego di batteri ipertermofili

  2013cites this paper
• Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus

  2013cites this paper
• Otimizac¸ ˜ ao de periodicidades fracas em genomas utilizando transformadas de Fourier e algoritmos gen´ eticos

  2013cites this paper
• Periplasmic Binding Proteins in Thermophiles: Characterization and Potential Application of an Arginine-Binding Protein from Thermotoga maritima: A Brief Thermo-Story

  2013cites this paper
• Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content

  2012cites this paper
• The Temperature Dependent Proteomic Analysis of Thermotoga maritima

  2012cites this paper
• Characterisation of proteins involved in CRISPR-mediated antiviral defence in Sulfolobus solfataricus

  2012cites this paper
• Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: how to relate microarray expression data with genomic sequences.

  2012cites this paper
• Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription.

  2011cites this paper
• Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups

  2011cites this paper
• PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences

  2011cites this paper
• Comparative community genomics in the Dead Sea: an increasingly extreme environment

  2010cites this paper
• Statistical analysis of conformational properties of periodic dinucleotide steps in nucleosomes

  2010cites this paper
• Bacterial infections associated with cancer: possible implication in etiology with special reference to lateral gene transfer

  2010cites this paper
• Comparative Analysis of Sequence Periodicity among Prokaryotic Genomes Points to Differences in Nucleoid Structure and a Relationship to Gene Expression

  2010cites this paper
• Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans

  2010cites this paper
• DNA photolyase of enterococci: possible explanation for its low sunlight inactivation rate

  2009cites this paper
• A Hybrid Technique for the Periodicity Characterization of Genomic Sequence Data

  2009cites this paper
• Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima.

  2009cites this paper
• ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets

  2009cites this paper
• Upstream curved sequences in E. coli are related to the regulation of transcription initiation

  2009cites this paper
• Phylogenetic signals in DNA composition: limitations and prospects.

  2009cites this paper
• Trehalose metabolism and signaling.

  2008cites this paper
• Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes

  2008influential citation
• Data compression and genomes: a two-dimensional life domain map.

  2008cites this paper
• A novel DNA sequence periodicity decodes nucleosome positioning

  2008cites this paper
• Revisiting the relationship between compositional sequence complexity and periodicity

  2008cites this paper
• Cloning and expression of a tauropine dehydrogenase from the marine sponge Suberites domuncula

  2008cites this paper
• Chromosome Architecture and Evolution in Bacteria

  2008cites this paper
• THE ORIGINS AND EVOLUTION OF HIGHLY CONSERVED GENE FAMILIES CONCERNED WITH BASIC CELLULAR AND DEVELOPMENT PROCESSES

  2008cites this paper
• Integrons in pseudomonads are associated with hotspots of genomic diversity

  2008cites this paper
• Functional Genomics in Thermophilic Microorganisms

  2007cites this paper
• A common topology for bacterial and eukaryotic transcription initiation?

  2007influential citation
• Primary sequences of proteins from complete genomes display a singular periodicity: Alignment-free N-gram analysis.

  2007cites this paper
• Do different surrogate methods detect lateral genetic transfer events of different relative ages?

  2006cites this paper
• Ten years of bacterial genome sequencing: comparative-genomics-based discoveries

  2006cites this paper
• Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.

  2006cites this paper
• Several Archaeal Homologs of Putative Oligopeptide-Binding Proteins Encoded by Thermotoga maritima Bind Sugars

  2006cites this paper
• DNA Motifs and Sequence Periodicities

  2006cites this paper
• Nucleic Acid and Protein Sequence Analysis and Bioinformatics

  2006cites this paper
• Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment

  2006influential citation
• Insights on the evolution of trehalose biosynthesis

  2006cites this paper
• Substrate Specificities and Expression Patterns Reflect the Evolutionary Divergence of Maltose ABC Transporters in Thermotoga maritima

  2005cites this paper
• DNA Bendability and Nucleosome Positioning in Transcriptional Regulation

  2005cites this paper
• Structure of the Mycobacterium tuberculosis flavin dependent thymidylate synthase (MtbThyX) at 2.0A resolution.

  2005cites this paper
• Review of signal processing in genetics

  2005cites this paper
• The Dynamic Bacterial Genome

  2005cites this paper
• Mathematical modeling of evolution of horizontally transferred genes.

  2005cites this paper
• OF SIGNAL PROCESSING IN GENETICS

  2005cites this paper
• Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance

  2005cites this paper
• Displacement of epsilon-proteobacterial core genes by horizontally transferred homologous genes.

  2005influential citation
• Periodicities of 10-11bp as indicators of the supercoiled state of genomic DNA.

  2004cites this paper
• Sequence periodicity of Escherichia coli is concentrated in intergenic regions

  2004cites this paper
• CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data

  2004influential citation
• Gene finding and the evaluation of synonymous codon usage features in microbial genomes

  2004cites this paper
• Cg 1 Pseudomonas putida plasmid from Naphthalene-Degrading Conjugal Transfer Region of the pCg 1 Identification and Characterization of the

  2003cites this paper
• Identification and Characterization of the Conjugal Transfer Region of the pCg1 plasmid from Naphthalene-Degrading Pseudomonas putida Cg1

  2003cites this paper
• How big is the iceberg of which organellar genes in nuclear genomes are but the tip?

  2003cites this paper
• Lateral gene transfer: when will adolescence end?

  2003cites this paper
• Determining the evolution of the aminoacyl-trna synthetases by the ratios of evolutionary distance method

  2002cites this paper
• Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission.

  2002cites this paper
• Horizontal Transfer of Naphthalene Catabolic Genes in a Toxic Waste Site

  2002cites this paper
• Spectral classification of archaeal and bacterial genomes

  2002cites this paper
• The Dynamics of Bacterial Genomes

  2002cites this paper
• Horizontal Gene Transfer and its Role in the Evolution of Prokaryotes

  2002cites this paper
• Regulation of Endo-Acting Glycosyl Hydrolases in the Hyperthermophilic Bacterium Thermotoga maritima Grown on Glucan- and Mannan-Based Polysaccharides

  2002cites this paper
• Statistical Dynamics of Clustering in the Genome Structure

  2002cites this paper
• On the Occurrence of Horizontal Gene Transfer Among an Arbitrarily Chosen Group of 26 Genes

  2002cites this paper
• Horizontal gene transfer in prokaryotes: quantification and classification.

  2001cites this paper
• On surrogate methods for detecting lateral gene transfer.

  2001cites this paper
• A DNA structural atlas for Escherichia coli.

  2000cites this paper
• Horizontal gene transfer among microbial genomes: new insights from complete genome analysis.

  2000cites this paper
• Assessing evolutionary relationships among microbes from whole-genome analysis.

  2000cites this paper
• Evidence of recent lateral gene transfer among hyperthermophilic Archaea

  2000cites this paper