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pseudomonadales_test.json
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{
"TF": "LexA",
"motifs": [
{
"protein_accession": "NP_418467.1",
"sites": [
"AACTGGTTTTATATACAGTA",
"TGCTGTGAGTATATACAGCA",
"TACTGTTTTTATATACAGTA",
"GGCTGTGGTTTTATACAGTC",
"TGCTGGATAGATATCCAGCG",
"TACTGTATGGATGTACAGTA",
"TACTGTTTATTTATACAGTA",
"TACTGTTTTTATATACAGTA",
"AACTGTATTTATATACAGTT",
"AACTGGTTTTATATACAGTA",
"AACTGTGATTTTATACAGTA",
"TGCTGTGAGTATATACAGCA",
"TACTGGTTATTTATACAGGT",
"AACTGTCGATACGTACAGTA",
"TACTGATGATATATACAGGT",
"TACTGTTTTTATATACAGTA",
"TACTGTATGAGCATACAGTA",
"TACTGTATATTCATTCAGGT",
"AACTGGACGTTTGTACAGCA",
"AACTGTTTTTTTATCCAGTA",
"AACTGGATAAAATTACAGGG",
"AACTGGATAATCATACAGTA",
"CACTGGTAAAGTATACAGTG",
"TGCTGTATGGATTAACAGGA",
"TGCTGGTTATCTATCCAGTG",
"GGCTGTGGTTTTATACAGTC",
"TGCTGGATAGATATCCAGCG",
"TATTGGCTGTTTATACAGTA",
"AGCTGGGTATATATACAGAT",
"TACTGGATATTTAAACAGGT",
"TCATGGTGTGTTATCCAGTA",
"TACTGGCTATTTCAACATGC",
"AAATGTTTTTACATCCACTA",
"AACTGGGGTAATATAGAGTT",
"AACTGGATAATCATACAGTA",
"AGCTGTTTATTTATACAGTG",
"CGCTGGGTTTTTAATCAGTT",
"TACTGTTTATTTATACAGTA",
"AGCTGTATTTGTCTCCAGTA",
"TACTGATGATATATACAGGT",
"TGCTGGTTATCTATCCAGTG",
"AACTGGATAAAATTACAGGG",
"TACTGTTTTTATATACAGTA",
"TACTGTATGAGCATACAGTA",
"TATAGGATTTTTATACAGTG",
"AACTGTCGATACGTACAGTA",
"AACTGGACGTTTGTACAGCA",
"GGCTGTGGTTTTATACAGTC",
"AGCTGAATAAATATACAGCA"
]
}
],
"input_parameters": {
"outputfile_name": "pseudo_test.json",
"dw_region": 0,
"maxID": 0.85,
"tax_ID": 135621,
"TF_family": "LexA",
"sleepy": 0.5,
"BLAST_eval": 1e-40,
"up_region": 250,
"selected_taxon": "species",
"min_cover": 0.8,
"BLAST_dbase": "nr",
"max_hits": 375
},
"cgb_parameters": {
"ancestral_state_reconstruction": false,
"maxPFAM": 2,
"hmmer_eval": 1e-07,
"COG_search": true,
"phylogenetic_weighting": true,
"operon_prediction_probability_threshold": 0.5,
"sleep": 1.5,
"heatmap_plot": true,
"site_count_weighting": true,
"network_size_plot": false,
"site_printout": false,
"OGejump": 5,
"eggNOG_dbname": "/home/k7n7vi/HMMERdbs/bact.hmmer",
"entrez_email": "[email protected]",
"NOG_search": false,
"PFAM_search": false,
"bootstrap_replicates": 10,
"TF_eval": 1e-11,
"PFAM_dbname": "/home/k7n7vi/HMMERdbs/Pfam-A.hmm",
"promoter_dw_distance": 50,
"operon_prediction_distance_tuning_parameter": 1.0,
"prior_regulation_probability": 0.03,
"alpha": 0.00285714285714,
"taxon_regulation_plot": false,
"maxCOG": 2,
"homolog_eval": 0.1,
"COG_dbname": "/home/k7n7vi/HMMERdbs/COG_database.hmm",
"motif_plot": true,
"entrez_apikey": "f87b172711faa816dce1073945384c090107",
"promoter_up_distance": 300,
"maxNOG": 2,
"posterior_probability_threshold_for_reporting": 0.975,
"gene_regulation_plot": false
}
}