Multiple genome alignment for identifying the core structure among moderately related microbial genomes (Q33381851)

26 July 2017

title

Multiple genome alignment for identifying the core structure among moderately related microbial genomes (English)

1 reference

26 July 2017

1

Ikuo Uchiyama

1 reference

26 July 2017

language of work or name

English

0 references

publication date

31 October 2008

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26 July 2017

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26 July 2017

volume

9

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26 July 2017

page(s)

515

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KEGG for linking genomes to life and the environment

26 July 2017

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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Mauve: multiple alignment of conserved genomic sequence with rearrangements

21 June 2018

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Biased biological functions of horizontally transferred genes in prokaryotic genomes

21 June 2018

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Genome-scale phylogeny and the detection of systematic biases

21 June 2018

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MAVID: constrained ancestral alignment of multiple sequences

21 June 2018

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Comparative genomics, minimal gene-sets and the last universal common ancestor

21 June 2018

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21 June 2018

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Neighbor-net: an agglomerative method for the construction of phylogenetic networks

21 June 2018

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Lateral Gene Transfer and the Origins of Prokaryotic Groups

21 June 2018

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Horizontal gene transfer and phylogenetics

21 June 2018

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The COG database: an updated version includes eukaryotes

21 June 2018

1 reference

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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

21 June 2018

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21 June 2018

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Essential Bacillus subtilis genes

21 June 2018

1 reference

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LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

21 June 2018

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The genetic core of the universal ancestor

21 June 2018

1 reference

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Ancient horizontal gene transfer

21 June 2018

1 reference

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MBGD: microbial genome database for comparative analysis

21 June 2018

1 reference

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Prokaryotic evolution in light of gene transfer

21 June 2018

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An approximately unbiased test of phylogenetic tree selection

21 June 2018

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Connected gene neighborhoods in prokaryotic genomes

21 June 2018

1 reference

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TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Genome-scale evolution: reconstructing gene orders in the ancestral species.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Horizontal gene transfer in prokaryotes: quantification and classification

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

A new implementation and detailed study of breakpoint analysis.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Gene context conservation of a higher order than operons.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Genome rearrangement by replication-directed translocation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Predicted highly expressed genes of diverse prokaryotic genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Lateral gene transfer and the nature of bacterial innovation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Horizontal gene transfer and the origin of species: lessons from bacteria.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Detecting alien genes in bacterial genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Phylogenetic classification and the universal tree

21 June 2018

1 reference

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Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Horizontal gene transfer among genomes: the complexity hypothesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Free recombination within Helicobacter pylori

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Molecular archaeology of the Escherichia coli genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

The effect of mismatch repair and heteroduplex formation on sexual isolation in Bacillus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Amelioration of bacterial genomes: rates of change and exchange

21 June 2018

1 reference

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Improved sensitivity of profile searches through the use of sequence weights and gap excision.

21 June 2018

1 reference

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 June 2018

1 reference

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Dependence of frequency of homologous recombination on the homology length.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Codon usage and tRNA content in unicellular and multicellular organisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

The neighbor-joining method: a new method for reconstructing phylogenetic trees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Homologous recombination in Escherichia coli: dependence on substrate length and homology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

The rapid generation of mutation data matrices from protein sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Evolutionary implications of the frequent horizontal transfer of mismatch repair genes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

Multiple genome rearrangement and breakpoint phylogeny.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2615449

31 October 2018

Identifiers

DOI

10.1186/1471-2164-9-515

1 reference

Dimensions Publication ID

26 July 2017

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-9-515

9 September 2019

1 reference

26 July 2017

1 reference