Examination of genome homogeneity in prokaryotes using genomic signatures

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Examination of genome homogeneity in prokaryotes using genomic signatures is …
instance of (P31):
scholarly articleQ13442814

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P819ADS bibcode2009PLoSO...4.8113B
P356DOI10.1371/JOURNAL.PONE.0008113
P8608Fatcat IDrelease_t2zbtkfyunb57dgdh4thodumjm
P932PMC publication ID2781299
P698PubMed publication ID19956556
P5875ResearchGate publication ID40443638

P50authorEystein SkjerveQ82949199
Jon BohlinQ42322490
P2860cites workAccelerated evolution associated with genome reduction in a free-living prokaryoteQ21999766
The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy numberQ22066393
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Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritimaQ22122435
Environments shape the nucleotide composition of genomesQ24489465
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applicationsQ24498207
GeneMark.hmm: new solutions for gene findingQ24546288
RNAmmer: consistent and rapid annotation of ribosomal RNA genesQ24675768
Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patternsQ24794642
Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.Q25256794
Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic virusesQ25257897
Basic local alignment search toolQ25938991
Origin of replication in circular prokaryotic chromosomesQ28292592
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeographyQ28764545
Amelioration of bacterial genomes: rates of change and exchangeQ29618260
Application of tetranucleotide frequencies for the assignment of genomic fragmentsQ33205791
Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomesQ33321678
Investigations of oligonucleotide usage variance within and between prokaryotesQ33329084
Global dinucleotide signatures and analysis of genomic heterogeneityQ33538671
Nitrogen-fixing aerobic bacteria have higher genomic GC content than non-fixing species within the same genus.Q52904226
Base composition bias might result from competition for metabolic resources.Q52940121
Sequence-dependent DNA structure: dinucleotide conformational mapsQ73329866
Sequence-dependent DNA structure: the role of the sugar-phosphate backboneQ74781286
Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acidQ79125877
GC content and genome length in Chargaff compliant genomesQ79437562
Formation and positioning of nucleosomes: effect of sequence-dependent long-range correlated structural disorderQ82548023
Codon usage between genomes is constrained by genome-wide mutational processesQ33976278
Microbial minimalism: genome reduction in bacterial pathogensQ34118332
Dinucleotide relative abundance extremes: a genomic signatureQ34289038
Evolutionary implications of microbial genome tetranucleotide frequency biasesQ34373303
Involvement of DNA curvature in intergenic regions of prokaryotesQ34594691
Bacterial pathogenomicsQ34702436
Compositional biases of bacterial genomes and evolutionary implicationsQ35624486
Genomic GC level, optimal growth temperature, and genome size in prokaryotes.Q36525252
Detecting horizontally transferred and essential genes based on dinucleotide relative abundanceQ36955997
Bacterial genome sequencing and its use in infectious diseasesQ36982025
Mono- through hexanucleotide composition of the Escherichia coli genome: a Markov chain analysisQ40565882
An environmental signature for 323 microbial genomes based on codon adaptation indicesQ42093922
Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction.Q42107461
Identification of coding and non-coding sequences using local Holder exponent formalismQ42665584
Ecophysiological significance of scale-dependent patterns in prokaryotic genomes unveiled by a combination of statistic and genometric analysesQ43736629
Bias of purine stretches in sequenced chromosomesQ44080398
Aerobiosis increases the genomic guanine plus cytosine content (GC%) in prokaryotesQ44108765
Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineagesQ47562989
Determination of bias in the relative abundance of oligonucleotides in DNA sequencesQ49219229
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue12
P407language of work or nameEnglishQ1860
P921main subjectprokaryotesQ19081
P304page(s)e8113
P577publication date2009-12-02
P1433published inPLOS OneQ564954
P1476titleExamination of genome homogeneity in prokaryotes using genomic signatures
P478volume4

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cites work (P2860)
Q34001815A quantitative account of genomic island acquisitions in prokaryotes
Q33851538Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage
Q34904516Amino acid usage is asymmetrically biased in AT- and GC-rich microbial genomes.
Q33657435Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
Q46361707Insights from the complete genome sequence of Clostridium tyrobutyricum provide a platform for biotechnological and industrial applications
Q35074674Microbial genomic taxonomy
Q33688556Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes
Q41303342Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines
Q34156218Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
Q34442010Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition
Q36277287The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes.

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