Synopsis

Bacterial chromosomes are highly polarized in their nucleotide composition through mutational selection related to replication. Using this compositional skews such as the GC skew, replication origin and terminus can be predicted in silico by observing the shift points. However, genome sequence is affected by the myriad of functional requirements and selection on numerous subgenomic features, and elimination of this "noise" should lead to better predictions. Here we present a noise reduction approach using low-pass filtering through Fast Fourier Transform coupled with cumulative skew graphs, which increases the prediction accuracy of the replication origin and terminus. Power spectral analysis elucidates that the mutational selection acting on the compositional skew of bacterial genomes are predominantly on the two replichores, regardless of the subgenomic properties including those of intergenic regions and horizontally transferred genes.



List of Genomes
[Bacteria] Acidobacteria bacterium Ellin345
[Bacteria] Acinetobacter sp. ADP1
[Archaea] Aeropyrum pernix K1
[Bacteria] Agrobacterium tumefaciens str. C58 chromosome circular
[Bacteria] Agrobacterium tumefaciens str. C58 chromosome linear
[Bacteria] Anabaena variabilis ATCC 29413
[Bacteria] Anaeromyxobacter dehalogenans 2CP-C
[Bacteria] Anaplasma marginale str. St. Maries
[Bacteria] Anaplasma phagocytophilum HZ
[Bacteria] Aquifex aeolicus VF5
[Archaea] Archaeoglobus fulgidus DSM 4304
[Bacteria] Aster yellows witches'-broom phytoplasma AYWB
[Bacteria] Azoarcus sp. EbN1
[Bacteria] Bacillus anthracis A2012
[Bacteria] Bacillus anthracis str. 'Ames Ancestor'
[Bacteria] Bacillus anthracis str. Ames
[Bacteria] Bacillus cereus ATCC 14579
[Bacteria] Bacillus cereus E33L
[Bacteria] Bacillus clausii KSM-K16
[Bacteria] Bacillus halodurans C-125
[Bacteria] Bacillus licheniformis ATCC 14580
[Bacteria] Bacillus subtilis subsp. subtilis str. 168
[Bacteria] Bacillus thuringiensis serovar konkukian str. 97-27
[Bacteria] Bacteroides fragilis NCTC 9343
[Bacteria] Bacteroides fragilis YCH46
[Bacteria] Bacteroides thetaiotaomicron VPI-5482
[Bacteria] Bartonella henselae str. Houston-1
[Bacteria] Bartonella quintana str. Toulouse
[Bacteria] Baumannia cicadellinicola str. Hc (Homalodisca coagulata)
[Bacteria] Bdellovibrio bacteriovorus HD100
[Bacteria] Bifidobacterium longum NCC2705
[Bacteria] Bordetella bronchiseptica RB50
[Bacteria] Bordetella parapertussis 12822
[Bacteria] Bordetella pertussis Tohama I
[Bacteria] Borrelia burgdorferi B31
[Bacteria] Borrelia garinii PBi chromosome linear
[Bacteria] Bradyrhizobium japonicum USDA 110
[Bacteria] Brucella abortus biovar 1 str. 9-941 chromosome I
[Bacteria] Brucella abortus biovar 1 str. 9-941 chromosome II
[Bacteria] Brucella melitensis 16M chromosome I
[Bacteria] Brucella melitensis 16M chromosome II
[Bacteria] Brucella melitensis biovar Abortus 2308 chromosome I
[Bacteria] Brucella melitensis biovar Abortus 2308 chromosome II
[Bacteria] Brucella suis 1330 chromosome I
[Bacteria] Brucella suis 1330 chromosome II
[Bacteria] Buchnera aphidicola str. APS (Acyrthosiphon pisum)
[Bacteria] Buchnera aphidicola str. Bp (Baizongia pistaciae)
[Bacteria] Buchnera aphidicola str. Sg (Schizaphis graminum)
[Bacteria] Burkholderia cenocepacia AU 1054 chromosome 1
[Bacteria] Burkholderia cenocepacia AU 1054 chromosome 2
[Bacteria] Burkholderia cenocepacia AU 1054 chromosome 3
[Bacteria] Burkholderia mallei ATCC 23344 chromosome 1
[Bacteria] Burkholderia mallei ATCC 23344 chromosome 2
[Bacteria] Burkholderia pseudomallei 1710b chromosome I
[Bacteria] Burkholderia pseudomallei 1710b chromosome II
[Bacteria] Burkholderia pseudomallei K96243 chromosome 1
[Bacteria] Burkholderia pseudomallei K96243 chromosome 2
[Bacteria] Burkholderia sp. 383 chromosome 1
[Bacteria] Burkholderia sp. 383 chromosome 2
[Bacteria] Burkholderia sp. 383 chromosome 3
[Bacteria] Burkholderia thailandensis E264 chromosome I
[Bacteria] Burkholderia thailandensis E264 chromosome II
[Bacteria] Burkholderia xenovorans LB400 chromosome 1
[Bacteria] Burkholderia xenovorans LB400 chromosome 2
[Bacteria] Burkholderia xenovorans LB400 chromosome 3
[Bacteria] Campylobacter jejuni RM1221
[Bacteria] Campylobacter jejuni subsp. jejuni NCTC 11168
[Bacteria] Candidatus Blochmannia floridanus
[Bacteria] Candidatus Blochmannia pennsylvanicus str. BPEN
[Bacteria] Candidatus Pelagibacter ubique HTCC1062
[Bacteria] Candidatus Protochlamydia amoebophila UWE25
[Bacteria] Carboxydothermus hydrogenoformans Z-2901
[Bacteria] Caulobacter crescentus CB15
[Bacteria] Chlamydia muridarum Nigg
[Bacteria] Chlamydia trachomatis A/HAR-13
[Bacteria] Chlamydia trachomatis D/UW-3/CX
[Bacteria] Chlamydophila abortus S26/3
[Bacteria] Chlamydophila caviae GPIC
[Bacteria] Chlamydophila felis Fe/C-56
[Bacteria] Chlamydophila pneumoniae AR39
[Bacteria] Chlamydophila pneumoniae CWL029
[Bacteria] Chlamydophila pneumoniae J138
[Bacteria] Chlamydophila pneumoniae TW-183
[Bacteria] Chlorobium chlorochromatii CaD3
[Bacteria] Chlorobium tepidum TLS
[Bacteria] Chromobacterium violaceum ATCC 12472
[Bacteria] Chromohalobacter salexigens DSM 3043
[Bacteria] Clostridium acetobutylicum ATCC 824
[Bacteria] Clostridium perfringens str. 13
[Bacteria] Clostridium tetani E88
[Bacteria] Colwellia psychrerythraea 34H
[Bacteria] Corynebacterium diphtheriae NCTC 13129
[Bacteria] Corynebacterium efficiens YS-314
[Bacteria] Corynebacterium glutamicum ATCC 13032
[Bacteria] Corynebacterium jeikeium K411
[Bacteria] Coxiella burnetii RSA 493
[Bacteria] Dechloromonas aromatica RCB
[Bacteria] Dehalococcoides ethenogenes 195
[Bacteria] Dehalococcoides sp. CBDB1
[Bacteria] Deinococcus geothermalis DSM 11300
[Bacteria] Deinococcus radiodurans R1 chromosome 1
[Bacteria] Deinococcus radiodurans R1 chromosome 2
[Bacteria] Desulfitobacterium hafniense Y51
[Bacteria] Desulfotalea psychrophila LSv54
[Bacteria] Desulfovibrio desulfuricans G20
[Bacteria] Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough
[Bacteria] Ehrlichia canis str. Jake
[Bacteria] Ehrlichia chaffeensis str. Arkansas
[Bacteria] Ehrlichia ruminantium str. Gardel
[Bacteria] Ehrlichia ruminantium str. Welgevonden
[Bacteria] Enterococcus faecalis V583
[Bacteria] Erwinia carotovora subsp. atroseptica SCRI1043
[Bacteria] Erythrobacter litoralis HTCC2594
[Bacteria] Escherichia coli CFT073
[Bacteria] Escherichia coli K12
[Bacteria] Escherichia coli O157:H7 EDL933
[Bacteria] Escherichia coli O157:H7 str. Sakai
[Bacteria] Escherichia coli UTI89
[Bacteria] Francisella tularensis subsp. holarctica
[Bacteria] Francisella tularensis subsp. tularensis Schu 4
[Bacteria] Frankia sp. CcI3
[Bacteria] Fusobacterium nucleatum subsp. nucleatum ATCC 25586
[Bacteria] Geobacillus kaustophilus HTA426
[Bacteria] Geobacter metallireducens GS-15
[Bacteria] Geobacter sulfurreducens PCA
[Bacteria] Gloeobacter violaceus PCC 7421
[Bacteria] Gluconobacter oxydans 621H
[Bacteria] Haemophilus ducreyi 35000HP
[Bacteria] Haemophilus influenzae 86-028NP
[Bacteria] Haemophilus influenzae Rd KW20
[Bacteria] Hahella chejuensis KCTC 2396
[Archaea] Haloarcula marismortui ATCC 43049 chromosome I
[Archaea] Haloarcula marismortui ATCC 43049 chromosome II
[Archaea] Halobacterium sp. NRC-1
[Bacteria] Helicobacter acinonychis str. Sheeba
[Bacteria] Helicobacter hepaticus ATCC 51449
[Bacteria] Helicobacter hepaticus ATCC 51449
[Bacteria] Helicobacter pylori 26695
[Bacteria] Helicobacter pylori HPAG1
[Bacteria] Helicobacter pylori J99
[Bacteria] Idiomarina loihiensis L2TR
[Bacteria] Jannaschia sp. CCS1
[Bacteria] Lactobacillus acidophilus NCFM
[Bacteria] Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842
[Bacteria] Lactobacillus johnsonii NCC 533
[Bacteria] Lactobacillus plantarum WCFS1
[Bacteria] Lactobacillus sakei subsp. sakei 23K
[Bacteria] Lactobacillus salivarius subsp. salivarius UCC118
[Bacteria] Lactococcus lactis subsp. lactis Il1403
[Bacteria] Lawsonia intracellularis PHE/MN1-00
[Bacteria] Legionella pneumophila str. Lens
[Bacteria] Legionella pneumophila str. Paris
[Bacteria] Legionella pneumophila subsp. pneumophila str. Philadelphia 1
[Bacteria] Leifsonia xyli subsp. xyli str. CTCB07
[Bacteria] Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
[Bacteria] Leptospira interrogans serovar Lai str. 56601 chromosome I
[Bacteria] Leptospira interrogans serovar Lai str. 56601 chromosome II
[Bacteria] Listeria innocua Clip11262
[Bacteria] Listeria monocytogenes EGD-e
[Bacteria] Listeria monocytogenes str. 4b F2365
[Bacteria] Magnetospirillum magneticum AMB-1
[Bacteria] Mannheimia succiniciproducens MBEL55E
[Bacteria] Mesoplasma florum L1
[Bacteria] Mesorhizobium loti MAFF303099
[Archaea] Methanocaldococcus jannaschii DSM 2661
[Archaea] Methanococcoides burtonii DSM 6242
[Archaea] Methanococcus maripaludis S2
[Archaea] Methanopyrus kandleri AV19
[Archaea] Methanosarcina acetivorans C2A
[Archaea] Methanosarcina barkeri str. fusaro chromosome 1
[Archaea] Methanosarcina mazei Go1
[Archaea] Methanosphaera stadtmanae DSM 3091
[Archaea] Methanospirillum hungatei JF-1
[Archaea] Methanothermobacter thermautotrophicus str. Delta H
[Bacteria] Methylobacillus flagellatus KT
[Bacteria] Methylococcus capsulatus str. Bath
[Bacteria] Moorella thermoacetica ATCC 39073
[Bacteria] Mycobacterium avium subsp. paratuberculosis K-10
[Bacteria] Mycobacterium bovis AF2122/97
[Bacteria] Mycobacterium leprae TN
[Bacteria] Mycobacterium sp. MCS
[Bacteria] Mycobacterium tuberculosis CDC1551
[Bacteria] Mycobacterium tuberculosis H37Rv
[Bacteria] Mycoplasma capricolum subsp. capricolum ATCC 27343
[Bacteria] Mycoplasma gallisepticum R
[Bacteria] Mycoplasma genitalium G37
[Bacteria] Mycoplasma hyopneumoniae 232
[Bacteria] Mycoplasma hyopneumoniae 7448
[Bacteria] Mycoplasma hyopneumoniae J
[Bacteria] Mycoplasma mobile 163K
[Bacteria] Mycoplasma mycoides subsp. mycoides SC str. PG1
[Bacteria] Mycoplasma penetrans HF-2
[Bacteria] Mycoplasma pneumoniae M129
[Bacteria] Mycoplasma pulmonis UAB CTIP
[Bacteria] Mycoplasma synoviae 53
[Bacteria] Myxococcus xanthus DK 1622
[Archaea] Nanoarchaeum equitans Kin4-M
[Archaea] Natronomonas pharaonis DSM 2160
[Bacteria] Neisseria gonorrhoeae FA 1090
[Bacteria] Neisseria meningitidis MC58
[Bacteria] Neisseria meningitidis Z2491
[Bacteria] Neorickettsia sennetsu str. Miyayama
[Bacteria] Nitrobacter hamburgensis X14
[Bacteria] Nitrobacter winogradskyi Nb-255
[Bacteria] Nitrosococcus oceani ATCC 19707
[Bacteria] Nitrosomonas europaea ATCC 19718
[Bacteria] Nitrosospira multiformis ATCC 25196 chromosome 1
[Bacteria] Nocardia farcinica IFM 10152
[Bacteria] Nostoc sp. PCC 7120
[Bacteria] Novosphingobium aromaticivorans DSM 12444
[Bacteria] Oceanobacillus iheyensis HTE831
[Bacteria] Onion yellows phytoplasma OY-M
[Bacteria] Pasteurella multocida subsp. multocida str. Pm70
[Bacteria] Pelobacter carbinolicus DSM 2380
[Bacteria] Pelodictyon luteolum DSM 273
[Bacteria] Photobacterium profundum SS9 chromosome 1
[Bacteria] Photobacterium profundum SS9 chromosome 2
[Bacteria] Photorhabdus luminescens subsp. laumondii TTO1
[Archaea] Picrophilus torridus DSM 9790
[Bacteria] Polaromonas sp. JS666
[Bacteria] Porphyromonas gingivalis W83
[Bacteria] Prochlorococcus marinus str. MIT 9312
[Bacteria] Prochlorococcus marinus str. MIT 9313
[Bacteria] Prochlorococcus marinus str. NATL2A
[Bacteria] Prochlorococcus marinus subsp. marinus str. CCMP1375
[Bacteria] Prochlorococcus marinus subsp. pastoris str. CCMP1986
[Bacteria] Propionibacterium acnes KPA171202
[Bacteria] Pseudoalteromonas atlantica T6c
[Bacteria] Pseudoalteromonas haloplanktis TAC125 chromosome I
[Bacteria] Pseudoalteromonas haloplanktis TAC125 chromosome II
[Bacteria] Pseudomonas aeruginosa PAO1
[Bacteria] Pseudomonas entomophila L48
[Bacteria] Pseudomonas fluorescens Pf-5
[Bacteria] Pseudomonas fluorescens PfO-1
[Bacteria] Pseudomonas putida KT2440
[Bacteria] Pseudomonas syringae pv. phaseolicola 1448A
[Bacteria] Pseudomonas syringae pv. syringae B728a
[Bacteria] Pseudomonas syringae pv. tomato str. DC3000
[Bacteria] Psychrobacter arcticus 273-4
[Bacteria] Psychrobacter cryohalolentis K5
[Archaea] Pyrobaculum aerophilum str. IM2
[Archaea] Pyrococcus abyssi GE5
[Archaea] Pyrococcus furiosus DSM 3638
[Archaea] Pyrococcus horikoshii OT3
[Bacteria] Ralstonia eutropha JMP134 chromosome 1
[Bacteria] Ralstonia eutropha JMP134 chromosome 2
[Bacteria] Ralstonia metallidurans CH34 chromosome 1
[Bacteria] Ralstonia metallidurans CH34 chromosome 2
[Bacteria] Ralstonia solanacearum GMI1000
[Bacteria] Rhizobium etli CFN 42
[Bacteria] Rhodobacter sphaeroides 2.4.1 chromosome 1
[Bacteria] Rhodobacter sphaeroides 2.4.1 chromosome 2
[Bacteria] Rhodoferax ferrireducens T118
[Bacteria] Rhodopirellula baltica SH 1
[Bacteria] Rhodopseudomonas palustris BisB18
[Bacteria] Rhodopseudomonas palustris BisB5
[Bacteria] Rhodopseudomonas palustris CGA009
[Bacteria] Rhodopseudomonas palustris HaA2
[Bacteria] Rhodospirillum rubrum ATCC 11170
[Bacteria] Rickettsia bellii RML369-C
[Bacteria] Rickettsia conorii str. Malish 7
[Bacteria] Rickettsia prowazekii str. Madrid E
[Bacteria] Rickettsia typhi str. Wilmington
[Bacteria] Rubrobacter xylanophilus DSM 9941
[Bacteria] Saccharophagus degradans 2-40
[Bacteria] Salinibacter ruber DSM 13855
[Bacteria] Salmonella enterica subsp. enterica serovar Choleraesuis str.
[Bacteria] Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC
[Bacteria] Salmonella enterica subsp. enterica serovar Typhi Ty2
[Bacteria] Salmonella enterica subsp. enterica serovar Typhi str. CT18
[Bacteria] Salmonella typhimurium LT2
[Bacteria] Shewanella denitrificans OS217
[Bacteria] Shewanella oneidensis MR-1
[Bacteria] Shigella boydii Sb227
[Bacteria] Shigella dysenteriae Sd197
[Bacteria] Shigella flexneri 2a str. 2457T
[Bacteria] Shigella flexneri 2a str. 301
[Bacteria] Shigella sonnei Ss046
[Bacteria] Silicibacter pomeroyi DSS-3
[Bacteria] Silicibacter sp. TM1040
[Bacteria] Sinorhizobium meliloti 1021
[Bacteria] Sodalis glossinidius str. 'morsitans'
[Bacteria] Staphylococcus aureus RF122
[Bacteria] Staphylococcus aureus subsp. aureus COL
[Bacteria] Staphylococcus aureus subsp. aureus MRSA252
[Bacteria] Staphylococcus aureus subsp. aureus MSSA476
[Bacteria] Staphylococcus aureus subsp. aureus MW2
[Bacteria] Staphylococcus aureus subsp. aureus Mu50
[Bacteria] Staphylococcus aureus subsp. aureus N315
[Bacteria] Staphylococcus aureus subsp. aureus NCTC 8325
[Bacteria] Staphylococcus aureus subsp. aureus USA300
[Bacteria] Staphylococcus epidermidis ATCC 12228
[Bacteria] Staphylococcus epidermidis RP62A
[Bacteria] Staphylococcus haemolyticus JCSC1435
[Bacteria] Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305
[Bacteria] Streptococcus agalactiae 2603V/R
[Bacteria] Streptococcus agalactiae A909
[Bacteria] Streptococcus agalactiae NEM316
[Bacteria] Streptococcus mutans UA159
[Bacteria] Streptococcus pneumoniae R6
[Bacteria] Streptococcus pneumoniae TIGR4
[Bacteria] Streptococcus pyogenes M1 GAS
[Bacteria] Streptococcus pyogenes MGAS10270
[Bacteria] Streptococcus pyogenes MGAS10394
[Bacteria] Streptococcus pyogenes MGAS10750
[Bacteria] Streptococcus pyogenes MGAS2096
[Bacteria] Streptococcus pyogenes MGAS315
[Bacteria] Streptococcus pyogenes MGAS5005
[Bacteria] Streptococcus pyogenes MGAS6180
[Bacteria] Streptococcus pyogenes MGAS8232
[Bacteria] Streptococcus pyogenes MGAS9429
[Bacteria] Streptococcus pyogenes SSI-1
[Bacteria] Streptococcus thermophilus CNRZ1066
[Bacteria] Streptococcus thermophilus LMG 18311
[Bacteria] Streptomyces avermitilis MA-4680
[Bacteria] Streptomyces coelicolor A3(2)
[Archaea] Sulfolobus acidocaldarius DSM 639
[Archaea] Sulfolobus solfataricus P2
[Archaea] Sulfolobus tokodaii str. 7
[Bacteria] Symbiobacterium thermophilum IAM 14863
[Bacteria] Synechococcus elongatus PCC 6301
[Bacteria] Synechococcus elongatus PCC 7942
[Bacteria] Synechococcus sp. CC9605
[Bacteria] Synechococcus sp. CC9902
[Bacteria] Synechococcus sp. JA-2-3B'a(2-13)
[Bacteria] Synechococcus sp. JA-3-3Ab
[Bacteria] Synechococcus sp. WH 8102
[Bacteria] Synechocystis sp. PCC 6803
[Bacteria] Syntrophus aciditrophicus SB
[Bacteria] Thermoanaerobacter tengcongensis MB4
[Bacteria] Thermobifida fusca YX
[Archaea] Thermococcus kodakarensis KOD1
[Archaea] Thermoplasma acidophilum DSM 1728
[Archaea] Thermoplasma volcanium GSS1
[Bacteria] Thermosynechococcus elongatus BP-1
[Archaea] Thermotoga maritima MSB8
[Bacteria] Thermus thermophilus HB27
[Bacteria] Thermus thermophilus HB8
[Bacteria] Thiobacillus denitrificans ATCC 25259
[Bacteria] Thiomicrospira crunogena XCL-2
[Bacteria] Thiomicrospira denitrificans ATCC 33889
[Bacteria] Treponema denticola ATCC 35405
[Bacteria] Treponema pallidum subsp. pallidum str. Nichols
[Bacteria] Tropheryma whipplei TW08/27
[Bacteria] Tropheryma whipplei str. Twist
[Bacteria] Ureaplasma parvum serovar 3 str. ATCC 700970
[Bacteria] Vibrio cholerae O1 biovar eltor str. N16961 chromosome I
[Bacteria] Vibrio cholerae O1 biovar eltor str. N16961 chromosome II
[Bacteria] Vibrio fischeri ES114 chromosome I
[Bacteria] Vibrio fischeri ES114 chromosome II
[Bacteria] Vibrio parahaemolyticus RIMD 2210633 chromosome I
[Bacteria] Vibrio parahaemolyticus RIMD 2210633 chromosome II
[Bacteria] Vibrio vulnificus CMCP6 chromosome I
[Bacteria] Vibrio vulnificus CMCP6 chromosome II
[Bacteria] Vibrio vulnificus YJ016 chromosome I
[Bacteria] Vibrio vulnificus YJ016 chromosome II
[Bacteria] Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis
[Bacteria] Wolbachia endosymbiont of Drosophila melanogaster
[Bacteria] Wolbachia endosymbiont strain TRS of Brugia malayi
[Bacteria] Wolinella succinogenes DSM 1740
[Bacteria] Xanthomonas axonopodis pv. citri str. 306
[Bacteria] Xanthomonas campestris pv. campestris str. 8004
[Bacteria] Xanthomonas campestris pv. campestris str. ATCC 33913
[Bacteria] Xanthomonas campestris pv. vesicatoria str. 85-10
[Bacteria] Xanthomonas oryzae pv. oryzae KACC10331
[Bacteria] Xanthomonas oryzae pv. oryzae MAFF 311018
[Bacteria] Xylella fastidiosa 9a5c
[Bacteria] Xylella fastidiosa Temecula1
[Bacteria] Yersinia pestis Antiqua
[Bacteria] Yersinia pestis CO92
[Bacteria] Yersinia pestis KIM
[Bacteria] Yersinia pestis Nepal516
[Bacteria] Yersinia pestis biovar Medievalis str. 91001
[Bacteria] Yersinia pseudotuberculosis IP 32953
[Bacteria] Zymomonas mobilis subsp. mobilis ZM4




(C) 2006 Institute for Advanced Biosciences, Keio University