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test_input.json
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{
"TF": "LexA",
"motifs": [
{
"name": "LexA_Mtu",
"genome_accessions": ["NC_000962.3"],
"protein_accession": "NP_217236.2",
"sites": [
"AAATCGAACATGTGTTCGAGTA",
"GTCTCGAACATGTGTTCGAGAA",
"GTATCGAACAATTGTTCGATAT",
"GAATCAAACATGTGTTCGACAG",
"TATTCGAACATGTATTCGAGTA",
"GTATCGAATATATTTTCGATGA",
"GAATCGAACAGGTGTTCGGCTA",
"AATTCGAACAAGTGATCGAATC",
"TGTTCGAAAATATGTTCGAAGT",
"ATCTCGAACATGTGTGCGATAC",
"ATCTCGAACATACGTTCGAGTA",
"CATTCGAATATGAGTTCGATCA",
"TTATCGCACATTCGTTCGATGG",
"GTATCGAACGATTGTTCGGAAA",
"GTATAGAACGGTTGTTCGAATA",
"CATTCGAATATTTGAGCGATGT",
"TATCCGAACATTTGATCGAAGC",
"TAGTCACTCATGTGTTCGATAT",
"TAATCGCTCGCGTGTTCGACAC",
"CTATCGAACGGGTGTTCTCTCA",
"TCTTCGAACAGACTTTCGTGCG",
"GATTCGAACATGTTAGCGAATA",
"GATTCGAACATGTTAGCGAATA",
"GTCTCGAACATGTGTTCGAGAA",
"ATCTCGAACATACGTTCGAGTA",
"GTATCGAACAATTGTTCGATAT",
"AAATCGAACATGTGTTCGAGTA",
"GTCTCGAACATGTGTTCGAGAA",
"GTATCGAACAATTGTTCGATAT",
"TACTCGAACGTATGTTCGAGAT",
"GTATCGAAAGTATGTTCGATCA",
"GTATCGAAAGTATGTTCGATCA",
"CCATCGAACGAATGTGCGATAA",
"TACTCGAATACATGTTCGAATA",
"ATCTCGAACATGTGTGCGATAC",
"GTATAGAACGGTTGTTCGAATA",
"GTATAGAACGGTTGTTCGAATA",
"GTATCGAACGATTGTTCGGAAA",
"GAATCAAACATGTGTTCGACAG",
"GAATCGAACAGGTGTTCGGCTA",
"TGTTCGAAAATATGTTCGAAGT",
"GAGTGGAACAGGTGTTCGAAAG",
"TATTGGAAAATTTGTTCTAAAA",
"CGTTCGAAAGTGTGAGCGGGTA",
"CAATCGAATAAATGTTCGAATA",
"TAATAGAACATATTATCGAACA",
"ATATTGAAGATATGTACGAGAT",
"CCTTCGAACATAGCATCGAACA",
"CCTTCGAACATAGCATCGAACA"
]
},
{
"name": "LexA_Cgl",
"genome_accessions": ["NC_006958.1"],
"protein_accession": "WP_003857389.1",
"sites": [
"TATGCGAACGTTTTTTCTAAAT",
"TGATCGCAATTGTGTGCTAAAA",
"TATTAAAACACTTGTTCTAAAC",
"TAGTCGAACATGTGAACGGTAT",
"AATACTGACAGAGGTTCGAATA",
"ATCTCGAACACTCGTACCATTT",
"ATTTCGAACAGTTGTGCGTGTA",
"TATTCGAAAACTTTTCCGATCA",
"AATTAGAACACTCCTACGAATA",
"TATTCGAACACGTGAGCGGGTA",
"TATTCGAACAGTTATTCGATTG",
"TAGTGGAAAATATGTTCGAGTG",
"TTTATGAAAATTTGTTTGAGGG",
"ACTTCGAAAAGTGGCTCCAAGC",
"CCATCAAACATTTGATCGGTGT",
"TTATAGAAAACTTGGACGAATC",
"ACCTCGAACACGTTTGTGTGGA",
"TTCTCGTAACCTTGTGCGAAAC",
"AGGGTGGACACTTATTCGAACG",
"AGTTCGAAAGTATTTCCGAACG",
"AGTTAGAACATATGTACCACTT",
"TGATAGAAAATATGTGCTATTT",
"CTTTTGAATAAGTGTTTGAATA",
"ATTTTAAAACTGTGTTCGGACA",
"GAAGCGAACAGAGTTTTTAGTG",
"TAAGAGAAACGGTGTTCGAAAA",
"CGATTGAACAAATGTTCGGGGT",
"TATTCAAATATGTGTTCGAATA",
"GAGTCGAACAGATGTGTAAATG",
"GGGGCAAAAATGTGTCCGACCA",
"GAATAGAAAAAATGTGCGAATA",
"TCCTCAAAAAAGTGGTCTAATG"
]
},
{
"name": "LexA_Lmo",
"genome_accessions": ["NC_003210.1"],
"protein_accession": "NP_464827.1",
"sites": [
"AAAAAGAATGTATGTTCGCTTT",
"AAAAAGAATGTATGTTCGCTTT",
"TGTACGAACGGTTGTTCTATAA",
"AAAGCGAACATTTATTCGTATT",
"ATATAGAACATACATTCGATTA",
"AAAACGAACAAGCGTTCTTATT",
"GTTGCGAACGTAGGTTCTGTGT",
"AAAAAGAAAGTGTGTTCGTGTT",
"TGATAAAACATATGTTCTGTTT",
"CATACAAACATTTGTTCTTATT",
"AAACCGAATATACGTTCTTATT",
"CCACCGAACATATGTTTTTATT",
"TTCAAGAACGTTTGTTCGTATA",
"AAAAAGAACGTATGTGCGAAAG",
"AAACCGAACATATTTTCGCATT",
"AATAAGAACATTTGTTCGTATA",
"TTTAAGAACGTTTGTTCGTATA"
]
},
{
"name": "LexA_Sau",
"genome_accessions": ["NC_007795.1"],
"protein_accession": "WP_001208760.1",
"sites": [
"AAATAGAACACGTGTTCGTATA",
"TTATAGAACATATGTTCGCTTT",
"AAAGCAAACGTTTGTTCGTAAA",
"TTTGCGAATATTTGTTCGTATA",
"AAAACAAACATTTGTTCGTTAA",
"ATATAGAACATTTGTTCGCTTT",
"CCTGCAAACGTACGTTCGTTTT",
"TATACGAACATGTGTTCTATTT",
"AAACAGAACATATGTTCGTATT",
"AACCCGAAAATATGTTTCGTGT"
]
},
{
"name": "LexA_Bsu",
"genome_accessions": ["NC_000964.3"],
"protein_accession": "NP_389668.1",
"sites": [
"TTACAGAACATTTGTTCCTCAC",
"CATAAGAACTCATGTTCGTGTA",
"CATAAGAACTCATGTTCGTGTA",
"ATAAAGAACATTCGTTCTTGTA",
"TGATAGAACGTATGTTTTGTAT",
"TATGGGAATGTACGTTCTGGAT",
"CTTGCGAATGCACGTTCTGTCA",
"TAAGGGAACGTTTGTTCTATTT",
"TAAGGGAACGTTTGTTCTATTT",
"CTTTCGAACGTTTGTTCTGTTT",
"TTAACGAACGTATGTTTGTAAA",
"AATCCGAATATGCGTTCGCTTT",
"AAAAAGAACGTTTGTTCGTATT",
"AACAGGAATGTTTGTTCGCATT",
"GACAGAAACGTTTGTTCGTATA",
"AGTACAAACATAGGTTCGAAAA",
"TATGAGAACGTATGTTTGTTTA",
"ACATCGAACTTTTGTTCTGGTT",
"ATAAGGAACGTTTGTTCTGTTG",
"AACGAGAACACTTGTTCCCTTT",
"ATGAAGAACGTTTGTTCTGTTA",
"AAAAGGAATATTCGTTCGGTAA",
"TATACGAATTTATGTTCTGTTT",
"TATGCGAAAGTATGTTCGTTTT",
"AAAAAGAACTTATGTTCGCTTT",
"CCTCCAAACTTTTGTTCTTTAT",
"TAACAGAACGATTGTTCTTATA",
"AAAGTTAACATATGTTCGCTTC",
"AACACGAACGTTTGTTTTTCTC",
"AAAAAGAACATTTGTTTCTTTT",
"CCACCGAACTTTAGTTCGTATT",
"AAAAAGAACACTTGTTCTGTTT",
"ATACCGAACGTATGTTTGCTTT",
"GTTAGGAATATACGTTCGTATA",
"CCGGAAAACGTAAGTTCGACTG",
"TCGTCGAAAACATGTTCGATGA",
"GTACCGAAACTTTGTTCGGGCA",
"AAACAGAACATAGGTTCCGCAG",
"AATAAAAACTTATGTTCGACTT",
"TTACAGAACATTTGTTCCTCAC"
]
},
{
"name": "LexA_Cdi",
"genome_accessions": ["NC_009089.1", "NC_008226.1"],
"protein_accession": "WP_003433043.1",
"sites": [
"TCTGCAAACATTTGTTCCTGAT",
"CAAGAGAACAAATGTTTGTAGA",
"CATAAAAACTTATGTTCTAAAT",
"GTCAGGAACTAATGTTCGAAAA",
"AAACAGAACAGTAGTTCCAGAA",
"GAATAGAACATAAAAATTTTAT",
"TTCTTGAACTTTAGTTTCTTCT",
"TTCCTTTTCAGATGTTCTTTTA",
"CTATAAAATAATAGTTCTGTTA",
"GTTATGAACTTAGGTTTCTCTC",
"AGAATGAACTATTGTTTTATTT",
"TAGCTGAACCAAAGTTCCAATC",
"TTTGTGAACCAATGTTTGATAT",
"AAATGGAACTTTAGTTCTATTT",
"TTGCAGAACGGGTGTTTTTTGA",
"TATAGGAACTTTAGTTCTTGGA"
]
}
],
"genomes": [
{
"name": "ace",
"accession_numbers": ["NC_008578.1"]
},
{
"name": "cgl",
"accession_numbers": ["NC_003450.3"]
},
{
"name": "lxy",
"accession_numbers": ["NC_006087.1"]
}
],
"prior_regulation_probability" : 0.03,
"alpha" : 0.00285714285714,
"promoter_up_distance" : 300,
"promoter_dw_distance" : 50,
"phylogenetic_weighting": true,
"site_count_weighting": true,
"posterior_probability_threshold_for_reporting": 0.975,
"operon_prediction_probability_threshold": 0.5,
"operon_prediction_distance_tuning_parameter" : 1.0,
"ancestral_state_reconstruction" : false,
"bootstrap_replicates" : 10,
"heatmap_plot" : true,
"motif_plot" : true,
"gene_regulation_plot" : false,
"taxon_regulation_plot" : false,
"network_size_plot" : false,
"site_printout" : false,
"entrez_email" : "[email protected]",
"entrez_apikey" : "YOUR_API_KEY",
"sleep" : 1.5,
"TF_eval" : 0.00000000001,
"homolog_eval" : 0.1,
"hmmer_eval" : 0.0000001,
"COG_search" : true,
"NOG_search" : false,
"PFAM_search" : false,
"COG_dbname" : "/home/YOURPATH/HMMERdbs/COG_database.hmm",
"eggNOG_dbname" : "/home/YOURPATH/HMMERdbs/bact.hmmer",
"PFAM_dbname" : "/home/YOURPATH/HMMERdbs/Pfam-A.hmm",
"OGejump" : 5,
"maxCOG" : 2,
"maxNOG" : 2,
"maxPFAM" : 2
}