PredictBias
identification of genomic and pathogenicity islands in prokaryotic genome
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Analyzed genomes
A) Input parameters
Genome
ex.gb
Threshold dinucleotide bias
2
Threshold codon bias
4
Threshold %GC bias
3
E-value (RPSBlast)
0.05
Genome (non-pathogenic)
B) Compare a potential GI or PAI in related non-pathogenic sp. (
phylogenetic tree
)
Potential GI or PAI start
end
Select Organism
Helicobacter pylori Cuz20
Prochlorococcus marinus str. NATL1A
Riemerella anatipestifer RA-CH-2
Shigella flexneri 1c
Streptococcus pyogenes MGAS315
Escherichia coli UTI89
Rhizobium etli CFN 42
Acinetobacter calcoaceticus
Listeria monocytogenes (unknown)
Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
Escherichia coli O157:H7 str. EDL933
Helicobacter pylori Lithuania75 (Helicobacter pylori Lit75)
Gbbct species
Helicobacter pylori Aklavik86
Escherichia coli BL21
Burkholderia cenocepacia MC0-3
Mycoplasma agalactiae PG2
Helicobacter pylori 35A
Vibrio campbellii ATCC BAA-1116
Escherichia coli APEC O1
Erysipelothrix rhusiopathiae str. Fujisawa
Streptococcus pyogenes MGAS10270
Helicobacter pylori SJM180
Corynebacterium sp. KPL1824
Yersinia pseudotuberculosis IP 31758
Staphylococcus aureus subsp. aureus COL
Macrococcus caseolyticus JCSC5402
Wolbachia endosymbiont of Onchocerca ochengi
Vibrio parahaemolyticus RIMD 2210633
Staphylococcus aureus subsp. aureus JH1
Helicobacter pylori HUP-B14
Ralstonia solanacearum CMR15
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC9150
Streptococcus pneumoniae CGSP14
Helicobacter pylori BM012S
Shewanella oneidensis MR-1
Acinetobacter baumannii AYE
Pseudovibrio species
Weizmannia coagulans
Yersinia pestis KIM10+
Borreliella burgdorferi JD1
Escherichia coli str. K-12 substr. MG1655
Helicobacter pylori 52
Shigella flexneri 5 str. 8401
Helicobacter pylori PeCan4
Carnobacterium maltaromaticum LMA28
Pseudomonas syringae pv. syringae B728a
Escherichia coli E24377A
Burkholderia multivorans ATCC 17616
Mycolicibacterium aurum
Clavibacter michiganensis subsp. michiganensis NCPPB 382
Helicobacter pylori Aklavik117
Staphylococcus aureus subsp. aureus ST228
Salinicoccus halodurans
Brucella ovis ATCC 25840
Rhodopseudomonas palustris BisB5
Helicobacter pylori Gambia94/24 (Helicobacter pylori Gam94/24)
Escherichia coli HS
Shewanella sp. Pdp11
Pseudomonas aeruginosa LESB58
Neisseria meningitidis MC58
Streptomyces atratus
Escherichia coli SMS-3-5
Streptococcus pyogenes MGAS5005
Rhodopseudomonas palustris HaA2
C. striatum 215
Streptococcus pyogenes SSI-1
Mycoplasma genitalium G37
Shewanella pealeana ATCC 700345
Burkholderia cenocepacia AU 1054
Streptococcus agalactiae A909
Pseudomonas aeruginosa PAO1
Streptococcus mitis B6
Mycoplasma arthritidis 158L3-1
Mycoplasma genitalium M2321
Bartonella tribocorum CIP 105476
Burkholderia ambifaria AMMD
Haemophilus influenzae Rd KW20
Pseudomonas aeruginosa PAK
Xanthomonas oryzae pv. oryzicola
Mycobacterium avium subsp. paratuberculosis K-10
Escherichia coli
Helicobacter pylori SNT49
Haemophilus influenzae PittGG
Pseudomonas putida
Borreliella burgdorferi B31
Vibrio vulnificus CMCP6
Shewanella sp. MR-7
Bacillus weihenstephanensis KBAB4
Haemophilus influenzae 86-028NP
Bacillus anthracis str. 'Ames Ancestor'
Helicobacter pylori UM066
Burkholderia vietnamiensis G4
Xanthomonas campestris pv. campestris str. 8004
Bacillus cereus ATCC 14579
Streptococcus equi subsp. equi 4047
Burkholderia thailandensis E264
Xanthomonas phaseoli pv. dieffenbachiae LMG 695
Helicobacter pylori 2017
Helicobacter pylori HPAG1
Escherichia coli CFT073
Streptococcus agalactiae 2603V/R
Helicobacter pylori Rif2
Helicobacter pylori Shi417
Francisella tularensis subsp. tularensis SCHU S4
Staphylococcus aureus subsp. aureus NCTC 8325
Klebsiella pneumoniae subsp. pneumoniae HS11286
Riemerella anatipestifer ATCC 11845
Helicobacter pylori 83
Helicobacter pylori PeCan18
Xanthomonas oryzae pv. oryzae
Proteus mirabilis HI4320
Acinetobacter baumannii ATCC 17978
Xanthomonas citri subsp. citri Aw12879
Staphylococcus aureus
Prochlorococcus marinus str. MIT 9313
Streptococcus agalactiae NEM316
Brucella melitensis bv. 1 str. 16M
Streptococcus thermophilus ASCC 1275
Borreliella burgdorferi N40
Pseudomonas syringae pv. tomato str. DC3000
Mycobacterium tuberculosis H37Rv
Lentibacter sp
Helicobacter pylori G27
Acinetobacter baumannii ACICU (unknown)
Helicobacter pylori F30
Helicobacter pylori Sat464
Streptococcus thermophilus
Collinsella intestinalis DSM 13280
Bradyrhizobium sp. ORS 278
Escherichia coli str. K-12 substr. DH10B
Synechocystis sp. PCC 6803
Shewanella baltica OS185
Helicobacter pylori SouthAfrica20
Mycobacterium marinum M
Borreliella burgdorferi CA382
Klebsiella pneumoniae
Prochlorococcus marinus str. NATL2A
Borreliella burgdorferi ZS7
Bacillus anthracis str. Sterne
Borreliella burgdorferi (Lyme disease spirochete)
Staphylococcus aureus subsp. aureus JH9
Helicobacter pylori
Helicobacter pylori P12
Burkholderia pseudomallei 1710b
Shewanella putrefaciens CN-32
Bifidobacterium animalis (Bifidobacterium lactis)
Vibrio cholerae O1 biovar El Tor str. N16961
Klebsiella pneumoniae CG43
Pseudomonas stutzeri RCH2
Helicobacter pylori 26695
Mycobacterium avium 104
Burkholderia pseudomallei 1106a
Pseudomonas syringae pv. phaseolicola 1448A
Mycobacterium ulcerans Agy99
Shewanella sp. MR-4
Acinetobacter oleivorans DR1
Helicobacter pylori Shi112
Helicobacter pylori OK310
Helicobacter pylori 2018
Bacillus anthracis str. Ames
Campylobacter concisus
Helicobacter pylori Rif1
Helicobacter pylori Puno120
Helicobacter pylori ELS37
Staphylococcus aureus subsp. aureus MW2
KBase_KBase
Shewanella halifaxensis HAW-EB4
Pseudomonas viridiflava CFBP 1590 isolate E12-5
Pseudomonas aeruginosa UCBPP-PA14
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Shigella flexneri 2a str. 301
Bacillus cereus ATCC 10987
Bacillus thuringiensis str. Al Hakam
Pseudomonas putida F1
Pseudomonas putida W619
Carnobacterium maltaromaticum
Salmonella enterica subsp. enterica serovar Typhi str. CT18
Enterococcus faecalis str. Symbioflor 1
Streptobacillus moniliformis DSM 12112
Riemerella anatipestifer RA-CH-1
Helicobacter pylori F32
Corynebacterium diphtheriae NCTC 13129
Pseudomonas aeruginosa
Salmonella enterica subsp. enterica serovar Choleraesuis str.SC-B67
Genus species
Akkermansia muciniphila
Burkholderia pseudomallei K96243
Mesorhizobium loti MAFF303099
Helicobacter pylori J99
Ralstonia solanacearum GMI1000
Rickettsia massiliae MTU5
Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Mycoplasma mycoides_cluster
Escherichia coli SE15
Shigella flexneri 2a str. 2457T
Streptococcus pyogenes MGAS2096
Campylobacter concisus 13826
Acinetobacter sp. ADP1
Parabacteroides goldsteinii
Brucella suis ATCC 23445
Staphylococcus warneri
Listeria monocytogenes EGD-e
Helicobacter pylori BM012A
Alkaliphilus metalliredigens QYMF
Escherichia coli O157:H7 str. Sakai
Staphylococcus aureus subsp. aureus USA300_FPR3757
Yersinia pseudotuberculosis IP 32953
Helicobacter pylori 51
Burkholderia mallei NCTC 10247
Streptococcus pyogenes MGAS10750
Desulfurobacterium thermolithotrophum DSM 11699
Shewanella baltica OS155
Lactobacillus plantarum WCFS1
Salmonella enterica subsp. enterica serovar Minnesota
Vibrio vulnificus YJ016
Frankia alni ACN14a
Sinorhizobium meliloti 1021
Pseudomonas aeruginosa DHS01
Streptococcus pyogenes M1 GAS
Staphylococcus aureus subsp. aureus Mu50
Rickettsia canadensis str. McKiel
Burkholderia lata
Gordonibacter urolithinfaciens
Staphylococcus aureus subsp. aureus Mu3
Streptococcus pyogenes MGAS8232
Aeromonas hydrophila subsp. hydrophila ATCC 7966
Xanthomonas campestris
Shewanella sp. ANA-3
Shigella dysenteriae Sd197
Helicobacter pylori F16
Helicobacter pylori B38
Helicobacter pylori India7 (Helicobacter pylori Ind7)
Shigella sonnei Ss046
Candidatus Saccharibacteria bacterium oral taxon 955
Pseudomonas aeruginosa PAO1 (Reference)
Wolbachia endosymbiont strain TRS of Brugia malayi
Helicobacter pylori 908
Streptococcus pneumoniae R6
Escherichia coli str. K-12 substr. W3110
Pseudomonas putida KT2440
Clostridioides difficile (Clostridium difficile)
Helicobacter pylori Shi470
Yersinia pseudotuberculosis YPIII
Corynebacterium glutamicum R
Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188
Thermotoga maritima MSB8 MSB8
Burkholderia pseudomallei 668
Acinetobacter calcoaceticus PHEA-2
Achromobacter xylosoxidans NH44784-1996
Clostridium botulinum A str. Hall
Bradyrhizobium sp. BTAi1
Helicobacter pylori F57
Helicobacter pylori v225d
Enterococcus faecium Aus0085
Wolbachia endosymbiont of Onchocerca volvulus str. Cameroon
Staphylococcus aureus subsp. aureus N315
Streptococcus pyogenes MGAS10394
Helicobacter pylori SouthAfrica7 (Helicobacter pylori SAfr7)
Burkholderia cenocepacia J2315
Helicobacter pylori B8
Helicobacter pylori UM037
Helicobacter pylori OK113
Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Yersinia pestis Angola
Shigella boydii Sb227
Escherichia coli 536
Pseudomonas putida GB-1
Streptococcus pneumoniae Hungary19A-6
Helicobacter pylori UM032
Helicobacter pylori XZ274
Staphylococcus species
Shewanella sp. W3-18-1
Burkholderia cenocepacia HI2424
Acinetobacter baumannii
Bordetella petrii DSM 12804
Bacillus halodurans C-125 C-125
Acinetobacter baumannii SDF
Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7
Corynebacterium glutamicum ATCC 13032
Agrobacterium rhizogenes (Rhizobium rhizogenes)
Candidatus Saccharimonas aalborgensis
Helicobacter pylori Puno135
Escherichia e.coli
Helicobacter pylori Shi169
Riemerella anatipestifer
Shewanella baltica OS195
Streptococcus sanguinis SK36
Burkholderia ambifaria MC40-6
C) Potential GIs and PAIs in NC_002516.2 (
download
)