PredictBias
identification of genomic and pathogenicity islands in prokaryotic genome
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Analyzed genomes
A) Input parameters
Genome
Cuz20.gbk
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
Borreliella burgdorferi (Lyme disease spirochete)
Bacillus anthracis str. Sterne
Shigella flexneri 1c
Helicobacter pylori
Staphylococcus aureus subsp. aureus JH9
Streptococcus pyogenes MGAS315
Burkholderia pseudomallei 1710b
Shewanella putrefaciens CN-32
Escherichia coli UTI89
Rhizobium etli CFN 42
Klebsiella pneumoniae CG43
Vibrio cholerae O1 biovar El Tor str. N16961
Acinetobacter calcoaceticus
Pseudomonas stutzeri RCH2
Listeria monocytogenes (unknown)
Mycobacterium avium 104
Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
Helicobacter pylori 26695
Pseudomonas syringae pv. phaseolicola 1448A
Burkholderia pseudomallei 1106a
Mycobacterium ulcerans Agy99
Escherichia coli O157:H7 str. EDL933
Acinetobacter oleivorans DR1
Shewanella sp. MR-4
Gbbct species
Helicobacter pylori Aklavik86
Escherichia coli BL21
Burkholderia cenocepacia MC0-3
Helicobacter pylori 2018
Mycoplasma agalactiae PG2
Helicobacter pylori 35A
Vibrio campbellii ATCC BAA-1116
Campylobacter concisus
Bacillus anthracis str. Ames
Staphylococcus aureus subsp. aureus MW2
KBase_KBase
Shewanella halifaxensis HAW-EB4
Escherichia coli APEC O1
Erysipelothrix rhusiopathiae str. Fujisawa
Pseudomonas aeruginosa UCBPP-PA14
Shigella flexneri 2a str. 301
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Bacillus cereus ATCC 10987
Streptococcus pyogenes MGAS10270
Bacillus thuringiensis str. Al Hakam
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
Pseudomonas putida F1
Ralstonia solanacearum CMR15
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC9150
Streptococcus pneumoniae CGSP14
Helicobacter pylori BM012S
Shewanella oneidensis MR-1
Pseudomonas putida W619
Carnobacterium maltaromaticum
Acinetobacter baumannii AYE
Salmonella enterica subsp. enterica serovar Typhi str. CT18
Pseudovibrio species
Enterococcus faecalis str. Symbioflor 1
Yersinia pestis KIM10+
Streptobacillus moniliformis DSM 12112
Borreliella burgdorferi JD1
Escherichia coli str. K-12 substr. MG1655
Helicobacter pylori 52
Shigella flexneri 5 str. 8401
Riemerella anatipestifer RA-CH-1
Carnobacterium maltaromaticum LMA28
Pseudomonas syringae pv. syringae B728a
Pseudomonas aeruginosa
Escherichia coli E24377A
Corynebacterium diphtheriae NCTC 13129
Burkholderia multivorans ATCC 17616
Genus species
Salmonella enterica subsp. enterica serovar Choleraesuis str.SC-B67
Mycolicibacterium aurum
Clavibacter michiganensis subsp. michiganensis NCPPB 382
Helicobacter pylori Aklavik117
Staphylococcus aureus subsp. aureus ST228
Akkermansia muciniphila
Salinicoccus halodurans
Brucella ovis ATCC 25840
Rhodopseudomonas palustris BisB5
Mesorhizobium loti MAFF303099
Burkholderia pseudomallei K96243
Ralstonia solanacearum GMI1000
Rickettsia massiliae MTU5
Mycoplasma mycoides_cluster
Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Escherichia coli HS
Escherichia coli SE15
Shewanella sp. Pdp11
Pseudomonas aeruginosa LESB58
Streptococcus pyogenes MGAS2096
Shigella flexneri 2a str. 2457T
Neisseria meningitidis MC58
Campylobacter concisus 13826
Acinetobacter sp. ADP1
Escherichia coli SMS-3-5
Brucella suis ATCC 23445
Staphylococcus warneri
Streptococcus pyogenes MGAS5005
Rhodopseudomonas palustris HaA2
C. striatum 215
Streptococcus pyogenes SSI-1
Helicobacter pylori BM012A
Alkaliphilus metalliredigens QYMF
Mycoplasma genitalium G37
Shewanella pealeana ATCC 700345
Escherichia coli O157:H7 str. Sakai
Yersinia pseudotuberculosis IP 32953
Staphylococcus aureus subsp. aureus USA300_FPR3757
Helicobacter pylori 51
Burkholderia cenocepacia AU 1054
Desulfurobacterium thermolithotrophum DSM 11699
Streptococcus pyogenes MGAS10750
Burkholderia mallei NCTC 10247
Lactobacillus plantarum WCFS1
Shewanella baltica OS155
Frankia alni ACN14a
Vibrio vulnificus YJ016
Salmonella enterica subsp. enterica serovar Minnesota
Sinorhizobium meliloti 1021
Streptococcus agalactiae A909
Pseudomonas aeruginosa PAO1
Streptococcus mitis B6
Mycoplasma arthritidis 158L3-1
Mycoplasma genitalium M2321
Bartonella tribocorum CIP 105476
Burkholderia ambifaria AMMD
Pseudomonas aeruginosa DHS01
Haemophilus influenzae Rd KW20
Pseudomonas aeruginosa PAK
Xanthomonas oryzae pv. oryzicola
Mycobacterium avium subsp. paratuberculosis K-10
Staphylococcus aureus subsp. aureus Mu50
Streptococcus pyogenes M1 GAS
Burkholderia lata
Rickettsia canadensis str. McKiel
Escherichia coli
Gordonibacter urolithinfaciens
Streptococcus pyogenes MGAS8232
Staphylococcus aureus subsp. aureus Mu3
Xanthomonas campestris
Aeromonas hydrophila subsp. hydrophila ATCC 7966
Haemophilus influenzae PittGG
Pseudomonas putida
Borreliella burgdorferi B31
Vibrio vulnificus CMCP6
Shewanella sp. ANA-3
Shigella dysenteriae Sd197
Shewanella sp. MR-7
Helicobacter pylori B38
Shigella sonnei Ss046
Bacillus weihenstephanensis KBAB4
Haemophilus influenzae 86-028NP
Wolbachia endosymbiont strain TRS of Brugia malayi
Bacillus anthracis str. 'Ames Ancestor'
Helicobacter pylori 908
Burkholderia vietnamiensis G4
Xanthomonas campestris pv. campestris str. 8004
Streptococcus pneumoniae R6
Escherichia coli str. K-12 substr. W3110
Bacillus cereus ATCC 14579
Streptococcus equi subsp. equi 4047
Burkholderia thailandensis E264
Xanthomonas phaseoli pv. dieffenbachiae LMG 695
Helicobacter pylori 2017
Pseudomonas putida KT2440
Escherichia coli CFT073
Streptococcus agalactiae 2603V/R
Yersinia pseudotuberculosis YPIII
Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188
Corynebacterium glutamicum R
Thermotoga maritima MSB8 MSB8
Francisella tularensis subsp. tularensis SCHU S4
Burkholderia pseudomallei 668
Staphylococcus aureus subsp. aureus NCTC 8325
Acinetobacter calcoaceticus PHEA-2
Klebsiella pneumoniae subsp. pneumoniae HS11286
Achromobacter xylosoxidans NH44784-1996
Bradyrhizobium sp. BTAi1
Clostridium botulinum A str. Hall
Riemerella anatipestifer ATCC 11845
Enterococcus faecium Aus0085
Helicobacter pylori 83
Wolbachia endosymbiont of Onchocerca volvulus str. Cameroon
Streptococcus pyogenes MGAS10394
Staphylococcus aureus subsp. aureus N315
Burkholderia cenocepacia J2315
Helicobacter pylori B8
Xanthomonas oryzae pv. oryzae
Proteus mirabilis HI4320
Yersinia pestis Angola
Acinetobacter baumannii ATCC 17978
Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Xanthomonas citri subsp. citri Aw12879
Staphylococcus aureus
Prochlorococcus marinus str. MIT 9313
Shigella boydii Sb227
Streptococcus agalactiae NEM316
Brucella melitensis bv. 1 str. 16M
Escherichia coli 536
Streptococcus thermophilus ASCC 1275
Borreliella burgdorferi N40
Pseudomonas syringae pv. tomato str. DC3000
Mycobacterium tuberculosis H37Rv
Pseudomonas putida GB-1
Lentibacter sp
Streptococcus pneumoniae Hungary19A-6
Acinetobacter baumannii ACICU (unknown)
Streptococcus thermophilus
Staphylococcus species
Collinsella intestinalis DSM 13280
Bradyrhizobium sp. ORS 278
Shewanella sp. W3-18-1
Acinetobacter baumannii
Burkholderia cenocepacia HI2424
Escherichia coli str. K-12 substr. DH10B
Bordetella petrii DSM 12804
Acinetobacter baumannii SDF
Bacillus halodurans C-125 C-125
Corynebacterium glutamicum ATCC 13032
Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7
Agrobacterium rhizogenes (Rhizobium rhizogenes)
Candidatus Saccharimonas aalborgensis
Synechocystis sp. PCC 6803
Escherichia e.coli
Shewanella baltica OS185
Mycobacterium marinum M
Borreliella burgdorferi CA382
Klebsiella pneumoniae
Riemerella anatipestifer
Streptococcus sanguinis SK36
Shewanella baltica OS195
Prochlorococcus marinus str. NATL2A
Borreliella burgdorferi ZS7
Burkholderia ambifaria MC40-6
C) Potential GIs and PAIs in CP002076 (
download
)