This search tools takes one index (reference) genome and returns a list of its proteins that match the criteria you specify in the following setup wizard.
Step 1: You have to specify the index strain and comparison strains to be used.
Step 2: You filter the protein list returned based on criteria specified for EACH comparison genome. Criteria can be that ortholog (i) must be in comparison genome ("Ortholog is present") (ii) must NOT be in the comparison genome ("Ortholog is absent") or (iii) does not matter ("Ortholog is optional").
Obtain a list of all protein-coding genes for index genome Pseudomonas aeruginosa LESB58 that are not found in other P. aeruginosa strains.
Index genome:
Pseudomonas aeruginosa LESB58
Comparison strains:
Pseudomonas aeruginosa 2192 ("Ortholog is absent" set in step 2)
Pseudomonas aeruginosa PACS2 ("Ortholog is absent" set in step 2)
Pseudomonas aeruginosa RP73 ("Ortholog is absent" set in step 2)
Pseudomonas aeruginosa B136-33 ("Ortholog is absent" set in step 2)
Pseudomonas aeruginosa M18 ("Ortholog is absent" set in step 2)
Pseudomonas aeruginosa DK2 ("Ortholog is absent" set in step 2)
Pseudomonas aeruginosa 39016 ("Ortholog is absent" set in step 2)
Pseudomonas aeruginosa NCGM2.S1 ("Ortholog is absent" set in step 2)
Pseudomonas aeruginosa PA7 ("Ortholog is absent" set in step 2)
Pseudomonas aeruginosa UCBPP-PA14 ("Ortholog is absent" set in step 2)
Pseudomonas aeruginosa PAO1 ("Ortholog is absent" set in step 2)
Obtain a list of all protein-coding genes shared by Pseudomonas aeruginosa strains that are not found in P. fluorescens, P. syringae, P. stutzeri and P. putida.
Index genome:
Pseudomonas aeruginosa PAO1
Comparison strains:
"Ortholog is present" is set in step 2 for following strains:
Pseudomonas aeruginosa 2192
Pseudomonas aeruginosa 39016
Pseudomonas aeruginosa B136-33
Pseudomonas aeruginosa C3719
Pseudomonas aeruginosa DK2
Pseudomonas aeruginosa LESB58
Pseudomonas aeruginosa M18
Pseudomonas aeruginosa NCGM2.S1
Pseudomonas aeruginosa PA7
Pseudomonas aeruginosa PACS2
Pseudomonas aeruginosa RP73
Pseudomonas aeruginosa UCBPP-PA14
"Ortholog is absent" is set in step 2 for following strains:
Pseudomonas fluorescens A506
Pseudomonas fluorescens F113
Pseudomonas fluorescens Pf0-1
Pseudomonas fluorescens SBW25
Pseudomonas putida BIRD-1
Pseudomonas putida DOT-T1E
Pseudomonas putida F1
Pseudomonas putida GB-1
Pseudomonas putida H8234
Pseudomonas putida HB3267
Pseudomonas putida KT2440
Pseudomonas putida NBRC 14164
Pseudomonas putida ND6
Pseudomonas putida S16
Pseudomonas putida W619
Pseudomonas stutzeri A1501
Pseudomonas stutzeri ATCC 17588 = LMG 11199
Pseudomonas stutzeri CCUG 29243
Pseudomonas stutzeri DSM 10701
Pseudomonas stutzeri DSM 4166
Pseudomonas stutzeri RCH2
Pseudomonas syringae pv. phaseolicola 1448A
Pseudomonas syringae pv. syringae B728a
Pseudomonas syringae pv. tomato str. DC3000