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OligoArrayDb Database: Pangenomic microarray probe sets
OligoArrayDb

The Source of Pangenomic Microarray Probe Sets

OligoArrayDb contains 8,974,726 microarray probes representing 3,187,065 CDS or transcripts from 977 organisms or strains

OligoArrayDb: pangenomic oligonucleotide microarray probe sets database
Jean - Marie Rouillard and Erdogan Gulari
Nucleic Acids Research 2009 37(Database issue):D938-41
[Abstract] [Full Text] [pdf]



The purpose of OligoArrayDb is to provide an easy access to pre-designed oligonucleotide microarray probes for researchers who would like to make their own microarrays. The database contains pangenomic microarray probe sets (45-mer) for most of the organisms with a fully sequenced genome, especially the ones that are unlikely to be covered by commercial microarrays. If someone decided it was worthwhile sequencing a given Archae, Bacteria or Eukaryotes, then we believe it is worth including it in OligoArrayDb to promote gene expression study on this organism using oligonucleotide microarrays. Please contact us if you would like your organism of interest added in OligoArrayDb if not yet present.

We retrieved annotated genomic sequences from public databases (Genbank, Ensembl, TIGR-JCVI) and used the latest version of the OligoArray software (Nucleic Acids Research, 2003, Vol. 31, No. 12 3057-3062 and Rouillard J.-M., unpublished data) to design probes targeting coding sequences (CDS or mRNA depending the source). Probe specificity is computed at the transcriptome level by predicting putative cross-hybridization with other transcript sequences using a thermodynamic model. Design parameters are tailored to each genome to take in account sequence properties like GC content. These parameters are accessible from each organism page. Probe design accuracy has been tested at transcriptome scale by co-designing probes targeting two organisms and hybridizing the resulting microarrays with aRNA samples derived from each organism. Here are the results and some details on the experiment design.

The content of this database is freely available. Just click on an organism name in the table below to get access to more specific details about the available probes and retreive the full set. If necessary, you can also download flat files as well as script to generate a local database.


: Organism inserted into the database during the last 30 days.           : Dataset modified during the last 30 days
Archaea
Bacteria
Eucaryotes
A C D H I M N P S T

A
    Aeropyrum pernix K1
    Archaeoglobus fulgidus DSM 4304

C
    Caldivirga maquilingensis IC-167
    Candidatus Korarchaeum cryptofilum OPF8
    Candidatus Methanoregula boonei 6A8

D
    Desulfurococcus kamchatkensis 1221n

H
    Haloarcula marismortui ATCC 43049
    Halobacterium salinarum R1
    Halomicrobium mukohataei DSM 12286
    Haloquadratum walsbyi
    Halorhabdus utahensis DSM 12940
    Halorubrum lacusprofundi ATCC 49239
    Hyperthermus butylicus DSM 5456

I
    Ignicoccus hospitalis KIN4/I

M
    Metallosphaera sedula DSM 5348
    Methanobrevibacter smithii ATCC 35061
    Methanocaldococcus fervens AG86
    Methanocaldococcus jannaschii DSM 2661
    Methanocaldococcus vulcanius M7
    Methanococcoides burtonii DSM 6242
    Methanococcus aeolicus Nankai-3
    Methanococcus maripaludis C5
    Methanococcus maripaludis C6
    Methanococcus maripaludis C7
    Methanococcus maripaludis S2
    Methanococcus vannielii SB
    Methanocorpusculum labreanum Z
    Methanoculleus marisnigri JR1
    Methanopyrus kandleri AV19
    Methanosaeta thermophila PT
    Methanosarcina acetivorans C2A
    Methanosarcina barkeri str. fusaro
    Methanosarcina mazei Go1
    Methanosphaera stadtmanae DSM 3091
    Methanosphaerula palustris E1-9c
    Methanospirillum hungatei JF-1

N
    Nanoarchaeum equitans Kin4-M
    Natronomonas pharaonis DSM 2160
    Nitrosopumilus maritimus SCM1

P
    Picrophilus torridus DSM 9790
    Pyrobaculum aerophilum str. IM2
    Pyrobaculum arsenaticum DSM 13514
    Pyrobaculum calidifontis JCM 11548
    Pyrobaculum islandicum DSM 4184
    Pyrococcus abyssi GE5
    Pyrococcus furiosus DSM 3638
    Pyrococcus horikoshii OT3

S
    Staphylothermus marinus F1
    Sulfolobus acidocaldarius DSM 639
    Sulfolobus islandicus L.S.2.15
    Sulfolobus islandicus M.14.25
    Sulfolobus islandicus M.16.27
    Sulfolobus islandicus M.16.4
    Sulfolobus islandicus Y.G.57.14
    Sulfolobus islandicus Y.N.15.51
    Sulfolobus solfataricus P2
    Sulfolobus tokodaii str. 7

T
    Thermococcus gammatolerans EJ3
    Thermococcus kodakarensis KOD1
    Thermococcus onnurineus NA1
    Thermococcus sibiricus MM 739
    Thermofilum pendens Hrk 5
    Thermoplasma acidophilum DSM 1728
    Thermoplasma volcanium GSS1
    Thermoproteus neutrophilus V24Sta

A B C D E F G H J K L M N O P R S T U V W X Y Z

A
    Acaryochloris marina MBIC11017
    Acetobacter pasteurianus IFO 3283-01
    Acholeplasma laidlawii PG-8A
    Acidimicrobium ferrooxidans DSM 10331
    Acidiphilium cryptum JF-5
    Acidithiobacillus ferrooxidans ATCC 23270
    Acidithiobacillus ferrooxidans ATCC 53993
    Acidobacteria bacterium Ellin345
    Acidobacterium capsulatum ATCC 51196
    Acidothermus cellulolyticus 11B
    Acidovorax avenae subsp. citrulli AAC00-1
    Acidovorax sp. JS42
    Acinetobacter baumannii AB0057
    Acinetobacter baumannii AB307-0294
    Acinetobacter baumannii ACICU
    Acinetobacter baumannii ATCC 17978
    Acinetobacter baumannii str. AYE
    Acinetobacter baumannii str. SDF
    Acinetobacter sp. ADP1
    Actinobacillus pleuropneumoniae L20
    Actinobacillus pleuropneumoniae serovar 3 str. JL03
    Actinobacillus pleuropneumoniae serovar 7 str. AP76
    Actinobacillus succinogenes 130Z
    Actinosynnema mirum DSM 43827
    Aeromonas hydrophila subsp. hydrophila ATCC 7966
    Aggregatibacter actinomycetemcomitans D11S-1
    Aggregatibacter aphrophilus NJ8700
    Agrobacterium radiobacter K84
    Agrobacterium tumefaciens str. C58
    Agrobacterium vitis S4
    Akkermansia muciniphila ATCC BAA-835
    Alcanivorax borkumensis SK2
    Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
    Aliivibrio salmonicida LFI1238
    Alkalilimnicola ehrlichei MLHE-1
    Alkaliphilus metalliredigens QYMF
    Alkaliphilus oremlandii OhILAs
    Alteromonas macleodii 'Deep ecotype'
    Ammonifex degensii KC4
    Anabaena variabilis ATCC 29413
    Anaerocellum thermophilum DSM 6725
    Anaerococcus prevotii DSM 20548
    Anaeromyxobacter dehalogenans 2CP-1
    Anaeromyxobacter dehalogenans 2CP-C
    Anaeromyxobacter sp. Fw109-5
    Anaeromyxobacter sp. K
    Anaplasma marginale str. Florida
    Anaplasma marginale str. St. Maries
    Anaplasma phagocytophilum HZ
    Anoxybacillus flavithermus WK1
    Arcobacter butzleri RM4018
    Aromatoleum aromaticum EbN1
    Arthrobacter aurescens TC1
    Arthrobacter chlorophenolicus A6
    Arthrobacter sp. FB24
    Aster yellows witches'-broom phytoplasma AYWB
    Atopobium parvulum DSM 20469
    Azoarcus sp. BH72
    Azoarcus sp. EbN1
    Azorhizobium caulinodans ORS 571
    Azotobacter vinelandii DJ

B
    Bacillus amyloliquefaciens FZB42
    Bacillus anthracis str. A0248
    Bacillus anthracis str. Ames
    Bacillus anthracis str. 'Ames Ancestor'
    Bacillus anthracis str. CDC 684
    Bacillus anthracis str. Sterne
    Bacillus cereus 03BB102
    Bacillus cereus AH187
    Bacillus cereus AH820
    Bacillus cereus ATCC 10987
    Bacillus cereus ATCC 14579
    Bacillus cereus B4264
    Bacillus cereus E33L
    Bacillus cereus G9842
    Bacillus cereus Q1
    Bacillus cereus subsp. cytotoxis NVH 391-98
    Bacillus clausii KSM-K16
    Bacillus halodurans C-125
    Bacillus licheniformis ATCC 14580
    Bacillus pumilus SAFR-032
    Bacillus subtilis subsp. subtilis str. 168
    Bacillus thuringiensis serovar konkukian str. 97-27
    Bacillus thuringiensis str. Al Hakam
    Bacillus weihenstephanensis KBAB4
    Bacteroides fragilis YCH46
    Bacteroides thetaiotaomicron VPI-5482
    Bacteroides vulgatus ATCC 8482
    Bartonella bacilliformis KC583
    Bartonella grahamii as4aup
    Bartonella henselae str. Houston-1
    Bartonella quintana str. Toulouse
    Bartonella tribocorum CIP 105476
    Baumannia cicadellinicola str. Hc (Homalodisca coagulata)
    Bdellovibrio bacteriovorus HD100
    Beijerinckia indica subsp. indica ATCC 9039
    Beutenbergia cavernae DSM 12333
    Bifidobacterium adolescentis ATCC 15703
    Bifidobacterium animalis subsp. lactis AD011
    Bifidobacterium animalis subsp. lactis Bl-04
    Bifidobacterium animalis subsp. lactis DSM 10140
    Bifidobacterium longum DJO10A
    Bifidobacterium longum NCC2705
    Bifidobacterium longum subsp. infantis ATCC 15697
    Blattabacterium sp. (Blattella germanica) str. Bge
    Blattabacterium sp. (Periplaneta americana) str. BPLAN
    Bordetella bronchiseptica RB50
    Bordetella parapertussis 12822
    Bordetella pertussis Tohama I
    Bordetella petrii
    Borrelia afzelii PKo
    Borrelia burgdorferi B31
    Borrelia burgdorferi ZS7
    Borrelia duttonii Ly
    Borrelia garinii PBi
    Borrelia hermsii DAH
    Borrelia recurrentis A1
    Borrelia turicatae 91E135
    Brachybacterium faecium DSM 4810
    Brachyspira hyodysenteriae WA1
    Bradyrhizobium sp. BTAi1
    Bradyrhizobium sp. ORS278
    Brevibacillus brevis NBRC 100599
    Brucella abortus S19
    Brucella canis ATCC 23365
    Brucella melitensis 16M
    Brucella melitensis ATCC 23457
    Brucella melitensis biovar Abortus
    Brucella microti CCM 4915
    Brucella ovis ATCC 25840
    Brucella suis 1330
    Brucella suis ATCC 23445
    Buchnera aphidicola str. 5A (Acyrthosiphon pisum)
    Buchnera aphidicola str. APS (Acyrthosiphon pisum)
    Buchnera aphidicola str. Bp (Baizongia pistaciae)
    Buchnera aphidicola str. Cc (Cinara cedri)
    Buchnera aphidicola str. Sg (Schizaphis graminum)
    Buchnera aphidicola str. Tuc7 (Acyrthosiphon pisum)
    Burkholderia ambifaria AMMD
    Burkholderia ambifaria MC40-6
    Burkholderia cenocepacia AU 1054
    Burkholderia cenocepacia HI2424
    Burkholderia cenocepacia J2315
    Burkholderia cenocepacia MC0-3
    Burkholderia glumae BGR1
    Burkholderia mallei ATCC 23344
    Burkholderia mallei NCTC 10229
    Burkholderia mallei NCTC 10247
    Burkholderia mallei SAVP1
    Burkholderia multivorans ATCC 17616 JGI
    Burkholderia multivorans ATCC 17616 Tohoku
    Burkholderia phymatum STM815
    Burkholderia phytofirmans PsJN
    Burkholderia pseudomallei 1106a
    Burkholderia pseudomallei 1710b
    Burkholderia pseudomallei 668
    Burkholderia pseudomallei MSHR346
    Burkholderia sp. 383
    Burkholderia thailandensis E264
    Burkholderia vietnamiensis G4
    Burkholderia xenovorans LB400

C
    Caldicellulosiruptor saccharolyticus DSM 8903
    Campylobacter concisus 13826
    Campylobacter curvus 525.92
    Campylobacter fetus subsp. fetus 82-40
    Campylobacter hominis ATCC BAA-381
    Campylobacter jejuni RM1221
    Campylobacter jejuni subsp. doylei 269.97
    Campylobacter jejuni subsp. jejuni 81116
    Campylobacter jejuni subsp. jejuni 81-176
    Campylobacter jejuni subsp. jejuni NCTC 11168
    Campylobacter lari RM2100
    Candidatus Accumulibacter phosphatis clade IIA str. UW-1
    Candidatus Amoebophilus asiaticus 5a2
    Candidatus Azobacteroides pseudotrichonymphae genomovar. CFP2
    Candidatus Blochmannia floridanus
    Candidatus Blochmannia pennsylvanicus str. BPEN
    Candidatus Carsonella ruddii PV
    Candidatus Desulforudis audaxviator MP104C
    Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)
    Candidatus Hodgkinia cicadicola Dsem
    Candidatus Koribacter versatilis Ellin345
    Candidatus Liberibacter asiaticus str. psy62
    Candidatus Pelagibacter ubique HTCC1062
    Candidatus Phytoplasma australiense
    Candidatus Phytoplasma mali
    Candidatus Protochlamydia amoebophila UWE25
    Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
    Candidatus Sulcia muelleri GWSS
    Candidatus Sulcia muelleri SMDSEM
    Candidatus Vesicomyosocius okutanii HA
    Capnocytophaga ochracea DSM 7271
    Carboxydothermus hydrogenoformans Z-2901
    Catenulispora acidiphila DSM 44928
    Caulobacter crescentus CB15
    Caulobacter crescentus NA1000
    Caulobacter sp. K31
    Cellvibrio japonicus Ueda107
    Chitinophaga pinensis DSM 2588
    Chlamydia muridarum Nigg
    Chlamydia trachomatis 434/Bu
    Chlamydia trachomatis A/HAR-13
    Chlamydia trachomatis B/TZ1A828/OT
    Chlamydia trachomatis D/UW-3/CX
    Chlamydia trachomatis Jali20
    Chlamydia trachomatis L2b/UCH-1/proctitis
    Chlamydophila abortus S26/3
    Chlamydophila caviae GPIC
    Chlamydophila pneumoniae AR39
    Chlamydophila pneumoniae CWL029
    Chlamydophila pneumoniae J138
    Chlamydophila pneumoniae TW-183
    Chlorobaculum parvum NCIB 8327
    Chlorobium chlorochromatii CaD3
    Chlorobium limicola DSM 245
    Chlorobium luteolum DSM 273
    Chlorobium phaeobacteroides BS1
    Chlorobium phaeobacteroides DSM 266
    Chlorobium tepidum TLS
    Chloroflexus aggregans DSM 9485
    Chloroflexus aurantiacus J-10-fl
    Chloroflexus sp. Y-400-fl
    Chloroherpeton thalassium ATCC 35110
    Chromobacterium violaceum ATCC 12472
    Chromohalobacter salexigens DSM 3043
    Citrobacter koseri ATCC BAA-895
    Clavibacter michiganensis subsp. michiganensis NCPPB 382
    Clostridium acetobutylicum ATCC 824
    Clostridium beijerinckii NCIMB 8052
    Clostridium botulinum A2 str. Kyoto
    Clostridium botulinum A3 str. Loch Maree
    Clostridium botulinum A str. ATCC 19397
    Clostridium botulinum A str. Hall
    Clostridium botulinum B1 str. Okra
    Clostridium botulinum Ba4 str. 657
    Clostridium botulinum B str. Eklund 17B
    Clostridium botulinum E3 str. Alaska E43
    Clostridium botulinum F str. Langeland
    Clostridium cellulolyticum H10
    Clostridium difficile CD196
    Clostridium difficile R20291
    Clostridium kluyveri DSM 555
    Clostridium kluyveri NBRC 12016
    Clostridium novyi NT
    Clostridium perfringens ATCC 13124
    Clostridium perfringens SM101
    Clostridium phytofermentans ISDg
    Clostridium tetani E88
    Clostridium thermocellum ATCC 27405
    Colwellia psychrerythraea 34H
    Comamonas testosteroni CNB-2
    Coprothermobacter proteolyticus DSM 5265
    Corynebacterium diphtheriae NCTC 13129
    Corynebacterium glutamicum ATCC 13032
    Corynebacterium glutamicum R
    Corynebacterium kroppenstedtii DSM 44385
    Corynebacterium urealyticum DSM 7109
    Coxiella burnetii CbuG_Q212
    Coxiella burnetii CbuK_Q154
    Coxiella burnetii Dugway 5J108-111
    Coxiella burnetii RSA 331
    Coxiella burnetii RSA 493
    Cronobacter turicensis
    Cryptobacterium curtum DSM 15641
    Cupriavidus taiwanensis
    Cyanothece sp. ATCC 51142
    Cyanothece sp. PCC 7424
    Cyanothece sp. PCC 7425
    Cyanothece sp. PCC 8801
    Cyanothece sp. PCC 8802
    Cytophaga hutchinsonii ATCC 33406

D
    Dechloromonas aromatica RCB
    Dehalococcoides ethenogenes 195
    Dehalococcoides sp. BAV1
    Dehalococcoides sp. CBDB1
    Dehalococcoides sp. VS
    Deinococcus deserti VCD115
    Deinococcus geothermalis DSM 11300
    Deinococcus radiodurans R1
    Delftia acidovorans SPH-1
    Desulfatibacillum alkenivorans AK-01
    Desulfitobacterium hafniense DCB-2
    Desulfitobacterium hafniense Y51
    Desulfobacterium autotrophicum HRM2
    Desulfococcus oleovorans Hxd3
    Desulfohalobium retbaense DSM 5692
    Desulfomicrobium baculatum DSM 4028
    Desulfotalea psychrophila LSv54
    Desulfotomaculum acetoxidans DSM 771
    Desulfotomaculum reducens MI-1
    Desulfovibrio desulfuricans G20
    Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774
    Desulfovibrio magneticus RS-1
    Desulfovibrio salexigens DSM 2638
    Desulfovibrio vulgaris str. 'Miyazaki F'
    Desulfovibrio vulgaris subsp. vulgaris DP4
    Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough
    Diaphorobacter sp. TPSY
    Dichelobacter nodosus VCS1703A
    Dickeya dadantii Ech703
    Dickeya zeae Ech1591
    Dictyoglomus thermophilum H-6-12
    Dictyoglomus turgidum DSM 6724
    Dinoroseobacter shibae DFL 12
    Dyadobacter fermentans DSM 18053

E
    Edwardsiella ictaluri 93-146
    Edwardsiella tarda EIB202
    Eggerthella lenta DSM 2243
    Ehrlichia canis str. Jake
    Ehrlichia chaffeensis str. Arkansas
    Ehrlichia ruminantium str. Gardel
    Ehrlichia ruminantium str. Welgevonden CIRAD
    Ehrlichia ruminantium str. Welgevonden USPA
    Elusimicrobium minutum Pei191
    Enterobacter sakazakii ATCC BAA-894
    Enterobacter sp. 638
    Enterococcus faecalis V583
    Erwinia carotovora subsp. atroseptica SCRI1043
    Erwinia tasmaniensis Et1/99
    Erythrobacter litoralis HTCC2594
    Escherichia coli 0127:H6 E2348/69
    Escherichia coli 536
    Escherichia coli 55989
    Escherichia coli APEC O1
    Escherichia coli BL21
    Escherichia coli BL21(DE3)
    Escherichia coli B str. REL606
    Escherichia coli BW2952
    Escherichia coli CFT073
    Escherichia coli C str. ATCC 8739
    Escherichia coli E24377A
    Escherichia coli ED1a
    Escherichia coli HS
    Escherichia coli IAI1
    Escherichia coli IAI39
    Escherichia coli K12
    Escherichia coli O103:H2 str. 12009
    Escherichia coli O111:H- str. 11128
    Escherichia coli O157:H7 str. EC4115
    Escherichia coli O157:H7 str. TW14359
    Escherichia coli O26:H11 str. 11368
    Escherichia coli S88
    Escherichia coli SE11
    Escherichia coli SECEC SMS-3-5
    Escherichia coli SMS-3-5
    Escherichia coli str. K12 substr. DH10B
    Escherichia coli str. K-12 substr. MG1655
    Escherichia coli str. K12 substr. MG1655
    Escherichia coli UMN026
    Escherichia coli UTI89
    Escherichia fergusonii
    Eubacterium eligens ATCC 27750
    Eubacterium rectale ATCC 33656
    Exiguobacterium sibiricum 255-15
    Exiguobacterium sp. AT1b

F
    Fervidobacterium nodosum Rt17-B1
    Fibrobacter succinogenes subsp. succinogenes S85
    Finegoldia magna ATCC 29328
    Flavobacteriaceae bacterium 3519-10
    Flavobacterium johnsoniae UW101
    Flavobacterium psychrophilum JIP02/86
    Francisella philomiragia subsp. philomiragia ATCC 25017
    Francisella tularensis subsp. holarctica
    Francisella tularensis subsp. holarctica FTNF002-00
    Francisella tularensis subsp. holarctica OSU18
    Francisella tularensis subsp. mediasiatica FSC147
    Francisella tularensis subsp. novicida U112
    Francisella tularensis subsp. tularensis FSC 198
    Francisella tularensis subsp. tularensis SCHU S4
    Francisella tularensis subsp. tularensis WY96-3418
    Frankia alni ACN14a
    Frankia sp. CcI3
    Frankia sp. EAN1pec
    Fusobacterium nucleatum subsp. nucleatum ATCC 25586

G
    Gemmatimonas aurantiaca T-27
    Geobacillus kaustophilus HTA426
    Geobacillus sp. WCH70
    Geobacillus sp. Y412MC10
    Geobacillus sp. Y412MC61
    Geobacillus thermodenitrificans NG80-2
    Geobacter bemidjiensis Bem
    Geobacter lovleyi SZ
    Geobacter metallireducens GS-15
    Geobacter sp. FRC-32
    Geobacter sp. M21
    Geobacter sulfurreducens PCA
    Geobacter uraniireducens Rf4
    Gluconacetobacter diazotrophicus PAl 5
    Gluconobacter oxydans 621H
    Gordonia bronchialis DSM 43247
    Gramella forsetii KT0803
    Granulobacter bethesdensis CGDNIH1

H
    Haemophilus ducreyi 35000HP
    Haemophilus influenzae 86-028NP
    Haemophilus influenzae PittEE
    Haemophilus influenzae PittGG
    Haemophilus influenzae Rd KW20
    Haemophilus parasuis SH0165
    Haemophilus somnus 129PT
    Haemophilus somnus 2336
    Haliangium ochraceum DSM 14365
    Halorhodospira halophila SL1
    Halothermothrix orenii H 168
    Halothiobacillus neapolitanus c2
    Helicobacter acinonychis str. Sheeba
    Helicobacter hepaticus ATCC 51449
    Helicobacter pylori 26695
    Helicobacter pylori B38
    Helicobacter pylori G27
    Helicobacter pylori HPAG1
    Helicobacter pylori J99
    Helicobacter pylori P12
    Helicobacter pylori Shi470
    Heliobacterium modesticaldum Ice1
    Herminiimonas arsenicoxydans
    Herpetosiphon aurantiacus ATCC 23779
    Hirschia baltica ATCC 49814
    Hydrogenobaculum sp. Y04AAS1
    Hyphomonas neptunium ATCC 15444

J
    Jannaschia sp. CCS1
    Janthinobacterium sp. Marseille
    Jonesia denitrificans DSM 20603

K
    Kangiella koreensis DSM 16069
    Kineococcus radiotolerans SRS30216
    Klebsiella pneumoniae 342
    Klebsiella pneumoniae NTUH-K2044
    Klebsiella pneumoniae subsp. pneumoniae MGH 78578
    Kocuria rhizophila DC2201
    Kosmotoga olearia TBF 19.5.1
    Kytococcus sedentarius DSM 20547

L
    Lactobacillus acidophilus NCFM
    Lactobacillus brevis ATCC 367
    Lactobacillus casei ATCC 334
    Lactobacillus casei BL23
    Lactobacillus delbrueckii subsp. bulgaricus
    Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
    Lactobacillus fermentum IFO 3956
    Lactobacillus gasseri ATCC 33323
    Lactobacillus helveticus DPC 4571
    Lactobacillus johnsonii FI9785
    Lactobacillus johnsonii NCC 533
    Lactobacillus plantarum JDM1
    Lactobacillus reuteri DSM 20016
    Lactobacillus reuteri F275
    Lactobacillus reuteri JCM 1112
    Lactobacillus rhamnosus GG
    Lactobacillus rhamnosus Lc 705
    Lactobacillus sakei subsp. sakei 23K
    Lactobacillus salivarius UCC118
    Lactococcus lactis subsp. cremoris MG1363
    Lactococcus lactis subsp. cremoris SK11
    Lactococcus lactis subsp. lactis Il1403
    Laribacter hongkongensis HLHK9
    Legionella pneumophila str. Corby
    Legionella pneumophila str. Lens
    Legionella pneumophila str. Paris
    Legionella pneumophila subsp. pneumophila str. Philadelphia 1
    Leifsonia xyli subsp. xyli str. CTCB07
    Leptospira biflexa serovar Patoc strain 'Patoc 1 (Ames)'
    Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
    Leptospira borgpetersenii serovar Hardjo-bovis JB197
    Leptospira borgpetersenii serovar Hardjo-bovis L550
    Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
    Leptospira interrogans serovar Lai str. 56601
    Leptothrix cholodnii SP-6
    Leptotrichia buccalis DSM 1135
    Leuconostoc citreum KM20
    Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
    Listeria monocytogenes Clip80459
    Listeria monocytogenes HCC23
    Listeria monocytogenes str. 4b F2365
    Listeria welshimeri serovar 6b str. SLCC5334
    Lysinibacillus sphaericus C3-41

M
    Macrococcus caseolyticus JCSC5402
    Magnetococcus sp. MC-1
    Magnetospirillum magneticum AMB-1
    Mannheimia succiniciproducens MBEL55E
    Maricaulis maris MCS10
    Marinobacter aquaeolei VT8
    Marinomonas sp. MWYL1
    Mesoplasma florum L1
    Mesorhizobium loti MAFF303099
    Mesorhizobium sp. BNC1
    Methylacidiphilum infernorum V4
    Methylibium petroleiphilum PM1
    Methylobacillus flagellatus KT
    Methylobacterium chloromethanicum CM4
    Methylobacterium extorquens AM1
    Methylobacterium extorquens DM4
    Methylobacterium extorquens PA1
    Methylobacterium nodulans ORS 2060
    Methylobacterium populi BJ001
    Methylobacterium radiotolerans JCM 2831
    Methylobacterium sp. 4-46
    Methylocella silvestris BL2
    Methylococcus capsulatus str. Bath
    Methylotenera mobilis JLW8
    Methylovorus sp. SIP3-4
    Micrococcus luteus NCTC 2665
    Microcystis aeruginosa NIES-843
    Moorella thermoacetica ATCC 39073
    Mycobacterium abscessus
    Mycobacterium avium 104
    Mycobacterium avium subsp. paratuberculosis K-10
    Mycobacterium bovis AF2122/97
    Mycobacterium bovis BCG str. Pasteur 1173P2
    Mycobacterium bovis BCG str. Tokyo 172
    Mycobacterium gilvum PYR-GCK
    Mycobacterium leprae Br4923
    Mycobacterium leprae TN
    Mycobacterium marinum M
    Mycobacterium smegmatis str. MC2 155
    Mycobacterium sp. JLS
    Mycobacterium sp. KMS
    Mycobacterium sp. MCS
    Mycobacterium tuberculosis CDC1551
    Mycobacterium tuberculosis F11
    Mycobacterium tuberculosis H37Ra
    Mycobacterium tuberculosis H37Rv
    Mycobacterium tuberculosis KZN 1435
    Mycobacterium ulcerans Agy99
    Mycobacterium vanbaalenii PYR-1
    Mycoplasma agalactiae PG2
    Mycoplasma arthritidis 158L3-1
    Mycoplasma capricolum subsp. capricolum ATCC 27343
    Mycoplasma conjunctivae
    Mycoplasma gallisepticum R
    Mycoplasma genitalium G37
    Mycoplasma hyopneumoniae 232
    Mycoplasma hyopneumoniae 7448
    Mycoplasma hyopneumoniae J
    Mycoplasma mobile 163K
    Mycoplasma mycoides subsp. mycoides SC str. PG1
    Mycoplasma penetrans HF-2
    Mycoplasma pneumoniae M129
    Mycoplasma pulmonis UAB CTIP
    Mycoplasma synoviae 53
    Myxococcus xanthus DK 1622

N
    Nakamurella multipartita DSM 44233
    Natranaerobius thermophilus JW/NM-WN-LF
    Nautilia profundicola AmH
    Neisseria gonorrhoeae FA 1090
    Neisseria gonorrhoeae NCCP11945
    Neisseria meningitidis 053442
    Neisseria meningitidis alpha14
    Neisseria meningitidis FAM18
    Neisseria meningitidis MC58
    Neisseria meningitidis Z2491
    Neorickettsia risticii str. Illinois
    Neorickettsia sennetsu str. Miyayama
    Nitratiruptor sp. SB155-2
    Nitrobacter hamburgensis X14
    Nitrobacter winogradskyi Nb-255
    Nitrosococcus oceani ATCC 19707
    Nitrosomonas europaea ATCC 19718
    Nitrosomonas eutropha C71
    Nitrosospira multiformis ATCC 25196
    Nocardia farcinica IFM 10152
    Nocardioides sp. JS614
    Nostoc punctiforme PCC 73102
    Novosphingobium aromaticivorans DSM 12444

O
    Oceanobacillus iheyensis HTE831
    Ochrobactrum anthropi ATCC 49188
    Oenococcus oeni PSU-1
    Oligotropha carboxidovorans OM5
    Onion yellows phytoplasma OY-M
    Opitutus terrae PB90-1
    Orientia tsutsugamushi str. Boryong
    Orientia tsutsugamushi str. Ikeda

P
    Paenibacillus sp. JDR-2
    Parabacteroides distasonis ATCC 8503
    Paracoccus denitrificans PD1222
    Parvibaculum lavamentivorans DS-1
    Pasteurella multocida subsp. multocida str. Pm70
    Pectobacterium carotovorum subsp. carotovorum PC1
    Pectobacterium wasabiae WPP163
    Pediococcus pentosaceus ATCC 25745
    Pedobacter heparinus DSM 2366
    Pelobacter carbinolicus DSM 2380
    Pelobacter propionicus DSM 2379
    Pelodictyon luteolum DSM 273
    Pelodictyon phaeoclathratiforme BU-1
    Pelotomaculum thermopropionicum SI
    Persephonella marina EX-H1
    Petrotoga mobilis SJ95
    Phenylobacterium zucineum HLK1
    Photobacterium profundum SS9
    Photorhabdus asymbiotica
    Photorhabdus luminescens subsp. laumondii TTO1
    Polaromonas naphthalenivorans CJ2
    Polaromonas sp. JS666
    Polynucleobacter necessarius STIR1
    Polynucleobacter necessarius subsp. asymbioticus QLW-P1DMWA-1
    Polynucleobacter sp. QLW-P1DMWA-1
    Porphyromonas gingivalis ATCC 33277
    Porphyromonas gingivalis W83
    Prochlorococcus marinus str. AS9601
    Prochlorococcus marinus str. MIT 9211
    Prochlorococcus marinus str. MIT 9215
    Prochlorococcus marinus str. MIT 9301
    Prochlorococcus marinus str. MIT 9303
    Prochlorococcus marinus str. MIT 9312
    Prochlorococcus marinus str. MIT 9313
    Prochlorococcus marinus str. MIT 9515
    Prochlorococcus marinus str. NATL1A
    Prochlorococcus marinus str. NATL2A
    Propionibacterium acnes KPA171202
    Prosthecochloris aestuarii DSM 271
    Prosthecochloris vibrioformis DSM 265
    Proteus mirabilis HI4320
    Pseudoalteromonas atlantica T6c
    Pseudoalteromonas haloplanktis TAC125
    Pseudomonas aeruginosa LESB58
    Pseudomonas aeruginosa PA7
    Pseudomonas aeruginosa PAO1
    Pseudomonas aeruginosa UCBPP-PA14
    Pseudomonas entomophila L48
    Pseudomonas fluorescens Pf0-1
    Pseudomonas fluorescens Pf-5
    Pseudomonas fluorescens PfO-1
    Pseudomonas mendocina ymp
    Pseudomonas putida F1
    Pseudomonas putida GB-1
    Pseudomonas putida KT2440
    Pseudomonas putida W619
    Pseudomonas stutzeri A1501
    Pseudomonas syringae pv. phaseolicola 1448A
    Pseudomonas syringae pv. syringae B728a
    Pseudomonas syringae pv. tomato str. DC3000
    Psychrobacter arcticus 273-4
    Psychrobacter cryohalolentis K5
    Psychrobacter sp. PRwf-1
    Psychromonas ingrahamii 37

R
    Ralstonia eutropha H16
    Ralstonia eutropha JMP134
    Ralstonia metallidurans CH34
    Ralstonia pickettii 12D
    Ralstonia pickettii 12J
    Ralstonia solanacearum
    Renibacterium salmoninarum ATCC 33209
    Rhizobium etli CIAT 652
    Rhizobium leguminosarum bv. trifolii WSM1325
    Rhizobium leguminosarum bv. trifolii WSM2304
    Rhizobium sp. NGR234
    Rhodobacter sphaeroides 2.4.1
    Rhodobacter sphaeroides ATCC 17025
    Rhodobacter sphaeroides ATCC 17029
    Rhodobacter sphaeroides KD131
    Rhodococcus erythropolis PR4
    Rhodococcus jostii RHA1
    Rhodococcus opacus B4
    Rhodococcus sp. RHA1
    Rhodoferax ferrireducens DSM 15236
    Rhodopirellula baltica SH 1
    Rhodopseudomonas palustris BisA53
    Rhodopseudomonas palustris BisB18
    Rhodopseudomonas palustris BisB5
    Rhodopseudomonas palustris CGA009
    Rhodopseudomonas palustris HaA2
    Rhodopseudomonas palustris TIE-1
    Rhodospirillum centenum SW
    Rhodospirillum rubrum ATCC 11170
    Rickettsia africae ESF-5
    Rickettsia akari str. Hartford
    Rickettsia bellii OSU 85-389
    Rickettsia bellii RML369-C
    Rickettsia canadensis str. McKiel
    Rickettsia conorii str. Malish 7
    Rickettsia felis URRWXCal2
    Rickettsia massiliae MTU5
    Rickettsia peacockii str. Rustic
    Rickettsia prowazekii str. Madrid E
    Rickettsia rickettsii str. Iowa
    Rickettsia rickettsii str. 'Sheila Smith'
    Rickettsia typhi str. Wilmington
    Roseiflexus castenholzii DSM 13941
    Roseiflexus sp. RS-1
    Roseobacter denitrificans OCh 114
    Rubrobacter xylanophilus DSM 9941
    Ruegeria pomeroyi DSS-3

S
    Saccharophagus degradans 2-40
    Saccharopolyspora erythraea NRRL 2338
    Salinibacter ruber DSM 13855
    Salinispora arenicola CNS-205
    Salinispora tropica CNB-440
    Salmonella enterica subsp. arizonae serovar 62:z4,z23:--
    Salmonella enterica subsp. enterica serovar Agona str. SL483
    Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853
    Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
    Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
    Salmonella enterica subsp. enterica serovar Heidelberg str. SL476
    Salmonella enterica subsp. enterica serovar Newport str. SL254
    Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7
    Salmonella enterica subsp. enterica serovar Typhi str. Ty2
    Salmonella enterica subsp. enterica serovar Typhi Ty2
    Serratia proteamaculans 568
    Shewanella amazonensis SB2B
    Shewanella baltica OS155
    Shewanella baltica OS185
    Shewanella baltica OS195
    Shewanella baltica OS223
    Shewanella denitrificans OS217
    Shewanella frigidimarina NCIMB 400
    Shewanella halifaxensis HAW-EB4
    Shewanella loihica PV-4
    Shewanella oneidensis MR-1
    Shewanella pealeana ATCC 700345
    Shewanella piezotolerans WP3
    Shewanella putrefaciens CN-32
    Shewanella sediminis HAW-EB3
    Shewanella sp. ANA-3
    Shewanella sp. MR-4
    Shewanella sp. MR-7
    Shewanella sp. W3-18-1
    Shewanella woodyi ATCC 51908
    Shigella boydii CDC 3083-94
    Shigella boydii Sb227
    Shigella flexneri 2a str. 2457T
    Shigella flexneri 2a str. 301
    Shigella flexneri 5 str. 8401
    Shigella sonnei Ss046
    Silicibacter pomeroyi DSS-3
    Silicibacter sp. TM1040
    Sinorhizobium medicae WSM419
    Sinorhizobium meliloti 1021
    Sodalis glossinidius str. 'morsitans'
    Solibacter usitatus Ellin6076
    Sorangium cellulosum 'So ce 56'
    Sphaerobacter thermophilus DSM 20745
    Sphingomonas wittichii RW1
    Sphingopyxis alaskensis RB2256
    Staphylococcus aureus RF122
    Staphylococcus aureus subsp. aureus COL
    Staphylococcus aureus subsp. aureus JH1
    Staphylococcus aureus subsp. aureus JH9
    Staphylococcus aureus subsp. aureus MRSA252
    Staphylococcus aureus subsp. aureus Mu3
    Staphylococcus aureus subsp. aureus NCTC 8325
    Staphylococcus aureus subsp. aureus str. Newman
    Staphylococcus aureus subsp. aureus USA300
    Staphylococcus aureus subsp. aureus USA300_FPR3757
    Staphylococcus aureus subsp. aureus USA300_TCH1516
    Staphylococcus carnosus subsp. carnosus TM300
    Staphylococcus epidermidis ATCC 12228
    Staphylococcus epidermidis RP62A
    Staphylococcus haemolyticus JCSC1435
    Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305
    Stenotrophomonas maltophilia K279a
    Stenotrophomonas maltophilia R551-3
    Streptococcus agalactiae 2603V/R
    Streptococcus agalactiae A909
    Streptococcus agalactiae NEM316
    Streptococcus dysgalactiae subsp. equisimilis GGS_124
    Streptococcus equi subsp. equi 4047
    Streptococcus equi subsp. zooepidemicus
    Streptococcus equi subsp. zooepidemicus MGCS10565
    Streptococcus gordonii str. Challis substr. CH1
    Streptococcus mutans UA159
    Streptococcus pneumoniae 70585
    Streptococcus pneumoniae CGSP14
    Streptococcus pneumoniae D39
    Streptococcus pneumoniae G54
    Streptococcus pneumoniae Hungary19A-6
    Streptococcus pneumoniae JJA
    Streptococcus pneumoniae P1031
    Streptococcus pneumoniae R6
    Streptococcus pneumoniae Taiwan19F-14
    Streptococcus pneumoniae TIGR4
    Streptococcus pyogenes M1 GAS
    Streptococcus pyogenes MGAS10270
    Streptococcus pyogenes MGAS10394
    Streptococcus pyogenes MGAS10750
    Streptococcus pyogenes MGAS2096
    Streptococcus pyogenes MGAS315
    Streptococcus pyogenes MGAS5005
    Streptococcus pyogenes MGAS6180
    Streptococcus pyogenes MGAS8232
    Streptococcus pyogenes MGAS9429
    Streptococcus pyogenes NZ131
    Streptococcus pyogenes SSI-1
    Streptococcus sanguinis SK36
    Streptococcus suis 05ZYH33
    Streptococcus suis 98HAH33
    Streptococcus suis BM407
    Streptococcus suis P1/7
    Streptococcus suis SC84
    Streptococcus thermophilus CNRZ1066
    Streptococcus thermophilus LMD-9
    Streptococcus thermophilus LMG 18311
    Streptococcus uberis 0140J
    Streptomyces avermitilis MA-4680
    Streptomyces griseus subsp. griseus NBRC 13350
    Sulfurihydrogenibium azorense Az-Fu1
    Sulfurihydrogenibium sp. YO3AOP1
    Sulfurospirillum deleyianum DSM 6946
    Sulfurovum sp. NBC37-1
    Symbiobacterium thermophilum IAM 14863
    Synechococcus sp. CC9311
    Synechococcus sp. CC9605
    Synechococcus sp. CC9902
    Synechococcus sp. JA-2-3B'a(2-13)
    Synechococcus sp. JA-3-3Ab
    Synechococcus sp. PCC 7002
    Synechococcus sp. RCC307
    Synechococcus sp. WH 7803
    Synechococcus sp. WH 8102
    Syntrophobacter fumaroxidans MPOB
    Syntrophomonas wolfei subsp. wolfei str. Goettingen
    Syntrophus aciditrophicus SB

T
    Teredinibacter turnerae T7901
    Thauera sp. MZ1T
    Thermanaerovibrio acidaminovorans DSM 6589
    Thermoanaerobacter pseudethanolicus ATCC 33223
    Thermoanaerobacter sp. X514
    Thermoanaerobacter tengcongensis MB4
    Thermobaculum terrenum ATCC BAA-798
    Thermobifida fusca YX
    Thermodesulfovibrio yellowstonii DSM 11347
    Thermomicrobium roseum DSM 5159
    Thermomonospora curvata DSM 43183
    Thermosipho africanus TCF52B
    Thermosipho melanesiensis BI429
    Thermotoga lettingae TMO
    Thermotoga maritima MSB8
    Thermotoga neapolitana DSM 4359
    Thermotoga petrophila RKU-1
    Thermotoga sp. RQ2
    Thermus thermophilus HB27
    Thermus thermophilus HB8
    Thioalkalivibrio sp. HL-EbGR7
    Thiobacillus denitrificans ATCC 25259
    Thiomicrospira crunogena XCL-2
    Thiomicrospira denitrificans ATCC 33889
    Tolumonas auensis DSM 9187
    Treponema denticola ATCC 35405
    Treponema pallidum subsp. pallidum SS14
    Treponema pallidum subsp. pallidum str. Nichols
    Trichodesmium erythraeum IMS101
    Tropheryma whipplei str. Twist
    Tropheryma whipplei TW08/27

U
    Ureaplasma parvum serovar 3 str. ATCC 27815
    Ureaplasma parvum serovar 3 str. ATCC 700970
    Ureaplasma urealyticum serovar 10 str. ATCC 33699

V
    Variovorax paradoxus S110
    Veillonella parvula DSM 2008
    Verminephrobacter eiseniae EF01-2
    Vibrio cholerae M66-2
    Vibrio cholerae MJ-1236
    Vibrio cholerae O1 biovar eltor str. N16961
    Vibrio cholerae O395
    Vibrio fischeri ES114
    Vibrio fischeri MJ11
    Vibrio harveyi ATCC BAA-1116
    Vibrio parahaemolyticus RIMD 2210633
    Vibrio splendidus LGP32
    Vibrio vulnificus CMCP6
    Vibrio vulnificus YJ016

W
    Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis
    Wolbachia endosymbiont of Culex quinquefasciatus Pel
    Wolbachia endosymbiont of Drosophila melanogaster
    Wolbachia endosymbiont strain TRS of Brugia malayi
    Wolbachia pipientis
    Wolbachia sp. wRi
    Wolinella succinogenes DSM 1740

X
    Xanthobacter autotrophicus Py2
    Xanthomonas axonopodis pv. citri str. 306
    Xanthomonas campestris pv. campestris
    Xanthomonas campestris pv. campestris str. 8004
    Xanthomonas campestris pv. campestris str. ATCC 33913
    Xanthomonas campestris pv. vesicatoria str. 85-10
    Xanthomonas oryzae pv. oryzae KACC10331
    Xanthomonas oryzae pv. oryzae MAFF 311018
    Xanthomonas oryzae pv. oryzae PXO99A
    Xylanimonas cellulosilytica DSM 15894
    Xylella fastidiosa 9a5c
    Xylella fastidiosa M12
    Xylella fastidiosa M23
    Xylella fastidiosa Temecula1

Y
    Yersinia enterocolitica subsp. enterocolitica 8081
    Yersinia pestis Angola
    Yersinia pestis Antiqua
    Yersinia pestis biovar Microtus str. 91001
    Yersinia pestis CO92
    Yersinia pestis Nepal516
    Yersinia pestis Pestoides F
    Yersinia pseudotuberculosis IP 31758
    Yersinia pseudotuberculosis IP 32953
    Yersinia pseudotuberculosis PB1/+
    Yersinia pseudotuberculosis YPIII

Z
    Zymomonas mobilis subsp. mobilis ZM4

A C D E K L P S T

A
    Aspergillus fumigatus Af293
    Aspergillus nidulans FGSC A4

C
    Candida glabrata CBS 138
    Cryptosporidium parvum Iowa II

D
    Debaryomyces hansenii CBS767

E
    Encephalitozoon cuniculi GB-M1

K
    Kluyveromyces lactis NRRL Y-1140

L
    Leishmania infantum JPCM5

P
    Pichia stipitis CBS 6054

S
    Saccharomyces cerevisiae

T
    Theileria parva strain Muguga


 

Contact: Jean-Marie Rouillard
 

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Last update: October 26th 2010.