Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models (Q39535813)

12 September 2017

Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models (English)

1 reference

12 September 2017

0 references

Pierre Nicolas

1 reference

12 September 2017

Laurent Bize

1 reference

12 September 2017

Florence Muri

1 reference

12 September 2017

Mark Hoebeke

1 reference

12 September 2017

François Rodolphe

1 reference

12 September 2017

S Dusko Ehrlich

1 reference

12 September 2017

Bernard Prum

1 reference

12 September 2017

Philippe Bessières

1 reference

12 September 2017

language of work or name

English

0 references

publication date

1 March 2002

1 reference

12 September 2017

Nucleic Acids Research

1 reference

12 September 2017

1 reference

12 September 2017

1 reference

12 September 2017

1418-1426

1 reference

Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Pathogenicity islands and the evolution of microbes

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Lateral gene transfer and the nature of bacterial innovation

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

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

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Isochores and the evolutionary genomics of vertebrates

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Shaping the genome--restriction-modification systems as mobile genetic elements.

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Codon usage and lateral gene transfer in Bacillus subtilis

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Genetic exchange between bacteria in the environment

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Transposon Tn21, flagship of the floating genome

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Molecular archaeology of the Escherichia coli genome

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

GeneMark.hmm: new solutions for gene finding

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

The complete genome sequence of the gram-positive bacterium Bacillus subtilis

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Micado—a network-oriented database for microbial genomes

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Prediction of complete gene structures in human genomic DNA

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Strategies for achieving high-level expression of genes in Escherichia coli

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Asymmetric substitution patterns in the two DNA strands of bacteria

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

A hidden Markov model that finds genes in E. coli DNA

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Detection of new genes in a bacterial genome using Markov models for three gene classes

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Codon usage in bacteria: correlation with gene expressivity

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Evidence for horizontal gene transfer in Escherichia coli speciation

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Horizontal gene transfer: evidence and possible consequences

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Resistance to arsenic compounds in microorganisms

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Characterization of PBSX, a defective prophage of Bacillus subtilis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Bacillus subtilis bacteriophage SPbeta: localization of the prophage attachment site, and specialized transduction

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Inactivation of antibiotics and the dissemination of resistance genes

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Segmentation of yeast DNA using hidden Markov models.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Bayesian inference on biopolymer models

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

How Salmonella became a pathogen

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Finding genes in DNA with a Hidden Markov Model.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Distribution, diversity and evolution of the bacterial mercury resistance (mer) operon

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Sequence analysis of the 308 degrees to 311 degrees segment of the Bacillus subtilis 168 chromosome, a region devoted to cell wall metabolism, containing non-coding grey holes which reveal chromosomal rearrangements

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Complete nucleotide sequence of a skin element excised by DNA rearrangement during sporulation in Bacillus subtilis

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Stochastic models for heterogeneous DNA sequences

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

SEGMENT: identifying compositional domains in DNA sequences.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of A = T and G = C.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=101363

Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis

2 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/11884641

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/11884641

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Universal replication biases in bacteria

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/11884641

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/30.6.1418

1 reference

12 September 2017

1 reference

12 September 2017

PubMed publication ID

11884641

1 reference