Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models

Nucleic Acids Research

Volumn 30, Issue 6, 2002, Pages 1418-1426

  Nicolas, Pierre ^a,b   Bize, Laurent ^c   Muri, Florence ^b   Hoebeke, Mark ^a   Rodolphe, François ^a   Ehrlich, S Dusko ^c   Prum, Bernard ^b   Bessières, Philippe ^a  

^a UNIVERSITÉ DE VERSAILLES SAINT QUENTIN EN YVELINES   (France)

^b CNRS   (France)

^c CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALGORITHM; ANTIBIOTIC RESISTANCE; ARTICLE; BACILLUS SUBTILIS; BACTERIAL CHROMOSOME; CATABOLISM; CHROMOSOME SIZE; CODON; CONTROLLED STUDY; DNA SEQUENCE; GENE EXPRESSION; GENE MAPPING; GENE SEQUENCE; GENE TRANSFER; GENETIC HETEROGENEITY; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROPHAGE; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); POSIBACTERIA; PROKARYOTA;

EID: 0037085737     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/30.6.1418     Document Type: Article

References (61)

1. Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes
2. Molecular archeology of the Escherichia coli genome
3. Asymmetric substitution patterns in the two DNA strands of bacteria
4. Horizontal gene transfer: Evidence and possible consequences
5. Pathogenicity islands of virulent bacteria: Structure, function and impact on microbial evolution
6. How Salmonella became a pathogen
7. Pathogenicity islands and the evolution of microbes
8. Inactivation of antibiotics and the dissemination of resistance genes
9. Distribution, diversity and evolution of the bacterial mercury resistance (mer) operon
10. Transposon Tn21, flagship of the floating genome
11. Resistance to arsenic compounds in microorganisms
12. Genetic exchange between bacteria in the environment
13. Selfish operons: The evolutionary impact of gene clustering in prokaryotes and eukaryotes
14. Lateral gene transfer and the nature of bacterial innovation
15. Horizontal gene transfer and the origin of species: Lessons from bacteria
16. The complete genome of the gram-positive bacterium Bacillus subtilis
17. Sequence analysis of the 308 to 311 segment of the Bacillus subtilis 168 chromosome, a region devoted to cell wall metabolism, containing non-coding grey holes which reveal chromosomal rearrangements
18. Codon usage and lateral gene transfer in Bacillus subtilis
19. Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes
20. Evidence for horizontal gene transfer in Escherichia coli speciation
21. Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
22. Stochastic models for heterogeneous DNA sequences
23. Comparison d'algorithmes d'identification de chaînes de Markov cachées et application à la détection de régions homogènes dans les séquences d'ADN
24. Searching gene transfers on Bacillus subtilis using hidden Markov models
25. Modelling bacterial genomes using hidden Markov models
26. Segmentation of yeast DNA using hidden Markov models
27. Detecting homogenous segments in DNA sequences by using hidden Markov models
28. Statistical methods for DNA sequence segmentation
29. Segment: Identifying compositional domains in DNA sequences
30. Bayesian inference on biopolymer models
31. Statistical inference for probabilistic functions of finite state Markov chains
32. Tutorial on hidden Markov models and selected applications in speech recognition
33. Parameter estimation for hidden Gibbs chains
34. Bayesian estimation of hidden Markov chains: A stochastic implementation
35. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
36. Bioinformatics. The Machine Learning Approach
37. Maximum likelihood from incomplete data via the EM algorithm
38. A hidden Markov model that finds genes in Escherichia coli DNA
39. Prediction of complete gene structures in human genomic DNA
40. Finding genes in DNA with a hidden Markov model
41. GeneMark.hmm: New solutions for gene finding
42. Micado-a network-oriented database for microbial genomes
43. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
44. Characterization of PBSX, a defective prophage of Bacillus subtilis
45. Complete nucleotide sequence of a skin element excised by DNA rearrangement during sporulation in Bacillus subtilis
46. Bacillus subtilis bacteriophage SPβ: Localization of the prophage attachment site and specialized transduction
47. Shaping the genome-restriction-modification systems as mobile genetic elements
48. Codon usage in bacteria: Correlation with gene expressivity
49. Strategies for achieving high-level expression of genes in Escherichia coli
50. Universal replication biases in bacteria
51. The contributions of replication orientation, gene direction and signal sequences to base-composition asymmetries in bacterial genomes
52. Asymmetric substitution patterns: A review of possible underlying mutational or selective mechanisms
53. Base composition skews, replication orientation and gene orientation in 12 prokaryote genomes
54. Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule A=T and G=C
55. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
56. Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis
57. Relationships between genomic G+C content, RNA secondary structures and optimal growth temperature in prokaryotes
58. Isochores and the evolutionary genomics of vertebrates
59. Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes
60. Detection of new genes in a bacterial genome using Markov models for three gene classes
61. GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions