-
1
-
-
0242500968
-
Informatics for unveiling hidden genome signatures
-
Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T: Informatics for unveiling hidden genome signatures. Genome Res 2003, 13:693-702.
-
(2003)
Genome Res.
, vol.13
, pp. 693-702
-
-
Abe, T.1
Kanaya, S.2
Kinouchi, M.3
Ichiba, Y.4
Kozuki, T.5
Ikemura, T.6
-
2
-
-
0035399931
-
Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
-
Karlin S: Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol 2001, 9:335-343.
-
(2001)
Trends Microbiol.
, vol.9
, pp. 335-343
-
-
Karlin, S.1
-
4
-
-
1842332701
-
Compositional biases of bacterial genomes and evolutionary implications
-
Karlin S, Mrazek J, Campbell A: Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 1997, 179:3899-3913.
-
(1997)
J. Bacteriol.
, vol.179
, pp. 3899-3913
-
-
Karlin, S.1
Mrazek, J.2
Campbell, A.3
-
5
-
-
0037315735
-
Evolutionary implications of microbial genome tetranucleotide frequency biases
-
Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ: Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res 2003, 13:145-155.
-
(2003)
Genome Res.
, vol.13
, pp. 145-155
-
-
Pride, D.T.1
Meinersmann, R.J.2
Wassenaar, T.M.3
Blaser, M.J.4
-
6
-
-
0034534314
-
Visualization of pathogenicity regions in bacteria
-
Friis C, Jensen LJ, Ussery DW: Visualization of pathogenicity regions in bacteria. Genetica 2000, 108: 7-51.
-
(2000)
Genetica
, vol.108
, pp. 47-51
-
-
Friis, C.1
Jensen, L.J.2
Ussery, D.W.3
-
8
-
-
0002576679
-
Identification of horizontally acquired elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis
-
Pride DT, Blaser MJ: Identification of horizontally acquired elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis. Genome Lett 2002, 1:2-15.
-
(2002)
Genome Lett.
, vol.1
, pp. 2-15
-
-
Pride, D.T.1
Blaser, M.J.2
-
9
-
-
0000992937
-
Patterns of genome organization in bacteria
-
Freeman JM, Plasterer TN, Berry A, Paton J: Patterns of genome organization in bacteria. Science 1998, 279:1827.
-
(1998)
Science
, vol.279
, pp. 1827
-
-
Freeman, J.M.1
Plasterer, T.N.2
Berry, A.3
Paton, J.4
-
10
-
-
0035077729
-
Genome organisation and chromatin structure in Escherichia coli
-
Ussery DW, Larsen TS, Wilkes KT, Friis C, Worning P, Krogh A, Brunak S: Genome organisation and chromatin structure in Escherichia coli. Biochimie 2001, 83:201-212.
-
(2001)
Biochimie
, vol.83
, pp. 201-212
-
-
Ussery, D.W.1
Larsen, T.S.2
Wilkes, K.T.3
Friis, C.4
Worning, P.5
Krogh, A.6
Brunak, S.7
-
11
-
-
0032173634
-
Global dinucleotide signatures and analysis of genomic heterogeneity
-
Karlin S: Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol 1998, 1: 98-610.
-
(1998)
Curr. Opin. Microbiol.
, vol.1
, pp. 598-610
-
-
Karlin, S.1
-
12
-
-
0036677661
-
Why are complementary DNA strands symmetric?
-
Baisne P-F, Hampson S, Baldi P: Why are complementary DNA strands symmetric? Bioinformatics 2002, 18:1021-1033.
-
(2002)
Bioinformatics
, vol.18
, pp. 1021-1033
-
-
Baisne, P.-F.1
Hampson, S.2
Baldi, P.3
-
13
-
-
0033639086
-
Sequence analysis by additive scales: DNA structure for sequences and repeats of all length
-
Baldi P, Baisne P-F: Sequence analysis by additive scales: DNA structure for sequences and repeats of all length. Bioinformatics 2000, 16:865-889.
-
(2000)
Bioinformatics
, vol.16
, pp. 865-889
-
-
Baldi, P.1
Baisne, P.-F.2
-
14
-
-
0000724617
-
Structure and function of nucleic acids as cell constituents
-
Chargaff E: Structure and function of nucleic acids as cell constituents. Fed Proc 1951, 10:344-360.
-
(1951)
Fed. Proc.
, vol.10
, pp. 344-360
-
-
Chargaff, E.1
-
15
-
-
0042814847
-
Methods for comparing sources of strand compositional asymmetry in microbial chromosomes
-
Baran RH, Ko H, Jernigan RW: Methods for comparing sources of strand compositional asymmetry in microbial chromosomes. DNA Res 2003, 30:85-95.
-
(2003)
DNA Res.
, vol.30
, pp. 85-95
-
-
Baran, R.H.1
Ko, H.2
Jernigan, R.W.3
-
16
-
-
0033935187
-
The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes
-
Tillier ER, Collins RA: The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol 2000, 50: 49-257.
-
(2000)
J. Mol. Evol.
, vol.50
, pp. 249-257
-
-
Tillier, E.R.1
Collins, R.A.2
-
17
-
-
0018143102
-
An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking
-
Ornstein RL, Rein R, Breen DL, MacElroy RD: An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking. Biopolymers 1978, 17: 341-2360.
-
(1978)
Biopolymers
, vol.17
, pp. 2341-2360
-
-
Ornstein, R.L.1
Rein, R.2
Breen, D.L.3
MacElroy, R.D.4
-
18
-
-
0030003963
-
Propeller twist of base-pairs and the conformational mobility of dinucleotide steps in DNA
-
Hassan MAE, Calladine CR: Propeller twist of base-pairs and the conformational mobility of dinucleotide steps in DNA. J Mol Biol 1996, 259:95-103.
-
(1996)
J. Mol. Biol.
, vol.259
, pp. 95-103
-
-
Hassan, M.A.E.1
Calladine, C.R.2
-
19
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson WK, Gorin AA, Lu X, Hock LM, Zhurkin VB: DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 1998, 95:11163-11168.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.3
Hock, L.M.4
Zhurkin, V.B.5
-
20
-
-
0032575756
-
DNA structure in human RNA polymerase II promoters
-
Pedersen AG, Baldi P, Brunak S, Chauvin Y: DNA structure in human RNA polymerase II promoters. J Mol Biol 1998, 281: 63-673.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 663-673
-
-
Pedersen, A.G.1
Baldi, P.2
Brunak, S.3
Chauvin, Y.4
-
21
-
-
0029039118
-
Sequence-dependent bending propensity of DNA as reveald by DNase I: Parameters for trinucleotides
-
Brukner I, Sánchez R, Suck D, Pongor S: Sequence-dependent bending propensity of DNA as reveald by DNase I: parameters for trinucleotides. EMBO J 1995, 14:1812-1818.
-
(1995)
EMBO J.
, vol.14
, pp. 1812-1818
-
-
Brukner, I.1
Sánchez, R.2
Suck, D.3
Pongor, S.4
-
22
-
-
0026758856
-
Base compositional structure of genomes
-
Fickett JW, Torney DC, Wolf DR: Base compositional structure of genomes. Genomics 1992, 13:1056-1064.
-
(1992)
Genomics
, vol.13
, pp. 1056-1064
-
-
Fickett, J.W.1
Torney, D.C.2
Wolf, D.R.3
-
23
-
-
0028828990
-
Relative role of primary sequence and (G+C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species
-
Forsdyke DR: Relative role of primary sequence and (G+C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species. J Mol Evol 1995, 41:573-581.
-
(1995)
J. Mol. Evol.
, vol.41
, pp. 573-581
-
-
Forsdyke, D.R.1
-
24
-
-
0034125366
-
Probabilistic and statistical properties of words: An overview
-
Reinert G, Schbath S, Waterman MS: Probabilistic and statistical properties of words: an overview. J Comp Biol 2000, 7:1-46.
-
(2000)
J. Comp. Biol.
, vol.7
, pp. 1-46
-
-
Reinert, G.1
Schbath, S.2
Waterman, M.S.3
-
25
-
-
0036267349
-
Complete Nucleotide Sequence of Plasmid Rts, 1: Implications for Evolution of Large Plasmid Genomes
-
Murata T, Ohnishi M, Ara T, Kaneko J, Han CG, Li YF, Takashima K, Nojima H, Nakayama K, Kaji A, et al.: Complete Nucleotide Sequence of Plasmid Rts, 1: Implications for Evolution of Large Plasmid Genomes. J Bacteriol 2002, 184:3194-3202.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 3194-3202
-
-
Murata, T.1
Ohnishi, M.2
Ara, T.3
Kaneko, J.4
Han, C.G.5
Li, Y.F.6
Takashima, K.7
Nojima, H.8
Nakayama, K.9
Kaji, A.10
-
26
-
-
0347285389
-
Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C
-
Klockgether J, Reva O, Larbig K, Tümmler B: Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C. J Bacteriol 2004, 186:518-534.
-
(2004)
J. Bacteriol.
, vol.186
, pp. 518-534
-
-
Klockgether, J.1
Reva, O.2
Larbig, K.3
Tümmler, B.4
-
27
-
-
0346997968
-
Structural comparison of the integrative and conjugative elements R391, pMERPH, R997, and SXT
-
Böltner D, Osborn AM: Structural comparison of the integrative and conjugative elements R391, pMERPH, R997, and SXT. Plasmid 2004, 51:12-23.
-
(2004)
Plasmid
, vol.51
, pp. 12-23
-
-
Böltner, D.1
Osborn, A.M.2
-
28
-
-
0032530804
-
The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O, 157:H7
-
Burland V, Shao Y, Perna NT, Plunkett G, Sofia HJ, Blattner FR: The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O, 157:H7. Nucleic Acids Res 1998, 26:4196-4204.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 4196-4204
-
-
Burland, V.1
Shao, Y.2
Perna, N.T.3
Plunkett, G.4
Sofia, H.J.5
Blattner, F.R.6
-
29
-
-
0033817109
-
Plasmid-located pathogenicity determinants of Serratia entomophila, the causal agent of amber disease of grass grub, show similarity to the insecticidal toxins of Photorhabdus luminescens
-
Hurst MRH, Glare TR, Jackson TA, Ronson CW: Plasmid-located pathogenicity determinants of Serratia entomophila, the causal agent of amber disease of grass grub, show similarity to the insecticidal toxins of Photorhabdus luminescens. J Bacteriol 2000, 182:5127-5138.
-
(2000)
J. Bacteriol.
, vol.182
, pp. 5127-5138
-
-
Hurst, M.R.H.1
Glare, T.R.2
Jackson, T.A.3
Ronson, C.W.4
-
30
-
-
0345687907
-
The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state
-
Strömsten NJ, Benson SD, Burnett RM, Bamford DH, Bamford JKH: The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state. J Bacteriol 2003, 185:6985-6989.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 6985-6989
-
-
Strömsten, N.J.1
Benson, S.D.2
Burnett, R.M.3
Bamford, D.H.4
Bamford, J.K.H.5
-
31
-
-
0032246556
-
Tailed bacteriophages: The order Caudovirales
-
Ackermann HW: Tailed bacteriophages: the order Caudovirales. Adv Virus Res 1998, 51:135-201.
-
(1998)
Adv. Virus Res.
, vol.51
, pp. 135-201
-
-
Ackermann, H.W.1
-
32
-
-
0038529820
-
1, the first streptococcal phage
-
1, the first streptococcal phage. J Bacteriol 2003, 185:3325-3332.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 3325-3332
-
-
Nelson, D.1
Schuch, R.2
Zhu, S.3
Tscherne, D.M.4
Fischetti, V.A.5
-
33
-
-
0038392706
-
Bacteriophage observations and evolution
-
Ackermann HW: Bacteriophage observations and evolution. Res Microbiol 2003, 154:245-251.
-
(2003)
Res. Microbiol.
, vol.154
, pp. 245-251
-
-
Ackermann, H.W.1
-
34
-
-
0035958667
-
Structural organisation of the head-to-tail interface of a bacterial virus
-
Lurz R, Orlova EV, Gunther D, Dube P, Droge A, Weise F, van Heel M, Tavares P: Structural organisation of the head-to-tail interface of a bacterial virus. J Mol Biol 2001, 310: 027-1037.
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 1027-1037
-
-
Lurz, R.1
Orlova, E.V.2
Gunther, D.3
Dube, P.4
Droge, A.5
Weise, F.6
van Heel, M.7
Tavares, P.8
-
35
-
-
0344863179
-
The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1
-
Alonso JC, Luder G, Stiege AC, Chai S, Weise F, Trautner TA: The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1. Gene 1997, 204: 01-212.
-
(1997)
Gene
, vol.204
, pp. 201-212
-
-
Alonso, J.C.1
Luder, G.2
Stiege, A.C.3
Chai, S.4
Weise, F.5
Trautner, T.A.6
-
36
-
-
0034536178
-
Genome organization and characterization of mycobacteriophage Bxb1
-
Mediavilla J, Jain S, Kriakov J, Michael E, Ford ME, Duda RL, Jacobs WR Jr, Hendrix RW, Hatfull GF: Genome organization and characterization of mycobacteriophage Bxb1. Mol Microbiol 2000, 38:955-970.
-
(2000)
Mol. Microbiol.
, vol.38
, pp. 955-970
-
-
Mediavilla, J.1
Jain, S.2
Kriakov, J.3
Michael, E.4
Ford, M.E.5
Duda, R.L.6
Jacobs Jr., W.R.7
Hendrix, R.W.8
Hatfull, G.F.9
-
37
-
-
0036933705
-
Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
-
Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VAP, Fouts DE, Gill SR, Pop M, Holmes M, et al.: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Envir Microbiol 2002, 4:799-808.
-
(2002)
Envir. Microbiol.
, vol.4
, pp. 799-808
-
-
Nelson, K.E.1
Weinel, C.2
Paulsen, I.T.3
Dodson, R.J.4
Hilbert, H.5
Martins dos Santos, V.A.P.6
Fouts, D.E.7
Gill, S.R.8
Pop, M.9
Holmes, M.10
-
38
-
-
0037310805
-
Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa
-
Van Sluys MA, de Oliveira MC, Monteiro-Vitorello CB, Miyaki CY, Furlan LR, Camargo LEA, da Silva ACR, Moon DH, Takita MA, Lemos EGM, et al.: Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J Bacteriol 2003, 185:1018-1026.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 1018-1026
-
-
Van Sluys, M.A.1
de Oliveira, M.C.2
Monteiro-Vitorello, C.B.3
Miyaki, C.Y.4
Furlan, L.R.5
Camargo, L.E.A.6
da Silva, A.C.R.7
Moon, D.H.8
Takita, M.A.9
Lemos, E.G.M.10
-
39
-
-
0036937356
-
Global features of the Pseudomonas putida KT2440 genome sequence
-
Weinel C, Nelson KE, Tümmler B: Global features of the Pseudomonas putida KT2440 genome sequence. Envir Microbiol 2002, 4:809-818.
-
(2002)
Envir. Microbiol.
, vol.4
, pp. 809-818
-
-
Weinel, C.1
Nelson, K.E.2
Tümmler, B.3
-
40
-
-
10044246531
-
Comparative genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2, 440: Orthologs, codon usage, repetitive extragenic palindromic elements, and oligonucleotide motif signatures
-
Weinel C, Ussery DW, Ohlsson H, Sicheritz-Ponten T, Kiewitz C, Tümmler B: Comparative genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2, 440: orthologs, codon usage, repetitive extragenic palindromic elements, and oligonucleotide motif signatures. Genome Lett 2002, 1:175-187.
-
(2002)
Genome Lett.
, vol.1
, pp. 175-187
-
-
Weinel, C.1
Ussery, D.W.2
Ohlsson, H.3
Sicheritz-Ponten, T.4
Kiewitz, C.5
Tümmler, B.6
-
41
-
-
0036723852
-
R, 391: A conjugative integrating mosaic comprised of phage, plasmid, and transposon elements
-
Böltner D, MacMahon C, Pembroke JT, Strike P, Osborn AM: R, 391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements. J Bacteriol 2002, 184:5158-5169.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 5158-5169
-
-
Böltner, D.1
MacMahon, C.2
Pembroke, J.T.3
Strike, P.4
Osborn, A.M.5
-
43
-
-
0038392697
-
Bacteriophages with tails: Chasing their origins and evolution
-
Hendrix RW, Hatfull GF, Smith MC: Bacteriophages with tails: chasing their origins and evolution. Res Microbiol 2003, 154:253-257.
-
(2003)
Res. Microbiol.
, vol.154
, pp. 253-257
-
-
Hendrix, R.W.1
Hatfull, G.F.2
Smith, M.C.3
-
44
-
-
0021109593
-
A Markov analysis of DNA sequences
-
Almagor H: A Markov analysis of DNA sequences. J Theor Biol 1983, 104:633-645.
-
(1983)
J. Theor. Biol.
, vol.104
, pp. 633-645
-
-
Almagor, H.1
-
45
-
-
84874647903
-
-
Python home page
-
Python home page [http://www.python.org/]
-
-
-
-
46
-
-
84874658377
-
-
NCBI home page
-
NCBI home page [http://www.ncbi.nlm.nih.gov/]
-
-
-
-
47
-
-
84874666687
-
-
Plasmid genome database
-
Plasmid genome database [http://www.genomics.ceh.ac.uk/plasmiddb/]
-
-
-
|