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CRISPR_definitions.py
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CRISPR_definitions.py
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#This file contains the CRISPR Type definitions by protein
#The format below is preserved, but can be edited appropriately to allow changing of the definitions
#Current implementation is based on:
# Makarova, et al. 2015 (Nat. Rev. Micro.)
# Makarova, et al. 2011 (Nat. Rev. Micro.) - Not all of these names are used
# Makarova, et al. 2015 (Biology Direct)
# Shmakov, et al. 2015 (Mol. Cell)
# Smargon, et al. 2017 (Mol. Cell)
# Harrington, Burstein, et al. 2017 (Nature)
#
#LAST HMMs UPDATE: August 2018
#Cas11 could include: Csa5 (I-A), Cse2 (I-E), Csm2 (III-A) and Cmr5 (III-B)
#Cas5 includes: cas5a, cas5d, cas5e, cas5h, cas5p, cas5, cmx5, CasD
#Cas7 includes: csa2, csd2, cse4, csh2, casC, csp1, cst2
#Cas8a1 includes: cmx1, cst1, csx8, csx13, NCXXC-CXXC
#Cas8a2 includes: Csa4, Csx9
#Cas9 could include: Csx12
CRISPR_types = {
"Type I-A":[["Cas6"],["Csa5"],["Cas7"],["Cas5"],["Cas8a1","Cas8a2","Csa4","Csx9"],["Cas3'"],["Cas3''"],["Cas2"],["Cas4","Csa1"],["Cas1"],["Cas4"]],
"Type I-B":[["Cas6"],["Cas8b1","Csh1"],["Cas7","Cst2"],["Cas5"],["Cas3"],["Cas4","Csa1"],["Cas1"],["Cas2"]],
"Type I-C":[["Cas3"],["Cas5"],["Cas8c","Csd1","Csp2"],["Cas7"],["Cas4","Csa1"],["Cas1"],["Cas2"]],
"Type I-U":[["Cas3"],["Cas8c"],["Cas7"],["Cas5","GSU0054"],["Cas6"],["Cas4","Csa1"],["Cas1"],["Cas2"]],
"Type I-D":[["Cas3'"],["Cas3''"],["Cas10d","Csc3"],["Cas7","Csc2"],["Cas5","Csc1"],["Cas6"],["Cas4"],["Cas1"],["Cas2"]],
"Type I-E":[["Cas3"],["Cas8e","Cse1"],["Cse2","CasB"],["Cas7","Cse4","CasC"],["Cas5","CasD"],["Cas6","Cse3","CasE"],["Cas1"],["Cas2"]],
"Type I-F":[["Cas1"],["Cas2","Cas3"],["Cas8f","Csy1"],["Cas5","Csy2"],["Cas7","Csy3"],["Cas6","Cas6f","Csy4"]],
"Type I-G":[["Cas6"],["Cas8a1","Cst1"],["Cas7","Cst2"],["Cas5","Cas5t"],["Cas3"],["Cas4"],["Cas1"],["Cas2"]],
"Type II-A":[["Cas9","Csn1"],["Cas1"],["Cas2"],["Csn2"]],
"Type II-B":[["Cas9","Csn1"],["Cas1"],["Cas2"],["Cas4","Csa1"],],
"Type II-C":[["Cas9","Csn1"],["Cas1"],["Cas2"]],
"Type III-A":[["Cas6"],["Cas10","Csm1"],["Csm2"],["Cas7","Csm3"],["Cas5","Csm4"],["Cas7","Csm5"],["Csm6"],["Cas1"],["Cas2"]],
"Type III-B":[["Cas7","Cmr1"],["Cas10"],["Cas5","Cmr4"],["Cmr5"],["Cas6"],["Cas7","Cmr6"],["Cas1"],["Cas2"]],
"Type III-C":[["Cas7","Cmr1"],["Cas7","Cmr6"],["Cas10"],["Cas7","Cmr4"],["Cmr5"],["Cas5","Cmr3"]],
"Type III-D":[["Cas10"],["Cas7","Csm3"],["Cas5","Csx10"],["Csm2"],["Cas7","Csm3"],["Cas7","Csm3"],["all1473"],["Cas7","Csm3"]],
"Type IV-A":[["dinG","Csf4"],["Csf1"],["Cas7","Csf2"],["Cas5","Csf3"]],
"Type V-A":[["Cas12a","Cpf1"],["Cas4","Csa1"],["Cas1"],["Cas2"]],
"Type V-B":[["Cas12b","c2c1"],["Cas1"],["Cas2"]],
"Type V-C":[["Cas12c","c2c3"],["Cas1"]],
"Type V-D":[["Cas12d","CasY"],["Cas1"]],
"Type V-E":[["Cas12e","CasX"],["Cas4"],["Cas1"],["Cas2"]],
"Type V-U1":[["c2c4"]],
"Type V-U2":[["c2c8"]],
"Type V-U3":[["c2c10"]],
"Type V-U4":[["c2c9"]],
"Type V-U5":[["c2c5"]],
"Type VI-A":[["Cas13a","c2c2"],["Cas1"],["Cas2"]],
"Type VI-B1":[["Cas13b1","c2c6"],["Csx27"]],
"Type VI-B2":[["Cas13b2","c2c6"],["Csx28"]],
"Type VI-C":[["Cas13c","c2c7"]],
"Type VI-D":[["Cas13d","c2c7"]]
}
Cas_proteins = {
"Csa1":["Type I-A","Type I-B","Type I-C","Type I-D","Type II-B","Type V-A","Type V-B","Type V-E",],
"Csa4":["Type I-A"],
"Csa5":["Type I-A"],
"Csc1":["Type I-D"],
"Csc2":["Type I-D"],
"Csc3":["Type I-D"],
"Csd1":["Type I-C"],
"Cse1":["Type I-E"],
"Cse2":["Type I-E"],
"Cse3":["Type I-E"],
"Cse4":["Type I-E"],
"Csh1":["Type I-B"],
"Csf1":["Type IV-A"],
"Csf2":["Type IV-A"],
"Csf3":["Type IV-A"],
"Csf4":["Type IV-A"],
"Csn2":["Type II-A"],
"Csp2":["Type I-C"],
"Csy1":["Type I-F"],
"Csy2":["Type I-F"],
"Csy3":["Type I-F"],
"Csy4":["Type I-F"],
"Csn1":["Type II-A","Type II-B","Type II-C"],
"Csm1":["Type III-A"],
"Csm2":["Type III-A","Type III-D"],
"Csm3":["Type III-A","Type III-D"],
"Csm4":["Type III-A"],
"Csm5":["Type III-A"],
"Csm6":["Type III-A"],
"Cst1":["Type I-G"],
"Cst2":["Type I-G","Type I-B"],
"Csx9":["Type I-A"],
"Csx10":["Type III-D"],
"Cmr1":["Type III-B","Type III-C"],
"Cmr3":["Type III-C"],
"Cmr4":["Type III-B","Type III-C"],
"Cmr5":["Type III-B","Type III-C"],
"Cmr6":["Type III-B","Type III-C"],
"GSU0054":["Type I-U"],
"all1473":["Type III-D"],
"dinG":["Type IV-A"],
"Cas4":["Type I-A","Type I-B","Type I-C","Type I-U","Type I-D","Type I-G","Type II-B","Type V-A","Type V-B"],
"Cas5":["Type I-A","Type I-B","Type I-C","Type I-U","Type I-D","Type I-E","Type I-F","Type I-G","Type III-A","Type III-B","Type III-C","Type III-D","Type IV-A"],
"Cas5t":["Type I-G"],
"Cas6":["Type I-A","Type I-B","Type I-U","Type I-D","Type I-E","Type I-F","Type I-G","Type III-A","Type III-B"],
"Cas6f":["Type I-F"],
"Cas7":["Type I-A","Type I-B","Type I-C","Type I-U","Type I-D","Type I-E","Type I-F","Type I-G","Type III-A","Type III-B","Type III-C","Type III-D","Type IV-A"],
"Cas8a1":["Type I-A","Type I-G"],
"Cas8a2":["Type I-A"],
"Cas8b1":["Type I-B"],
"Cas8c": ["Type I-C","Type I-U"],
"Cas8e": ["Type I-E"],
"Cas8f": ["Type I-F"],
"Cas9":["Type II-A","Type II-B","Type II-C"],
"Cas10":["Type III-A","Type III-B","Type III-C","Type III-D"],
"Cas10d":["Type I-D"],
"CasB":["Type I-E"],
"CasD":["Type I-E"],
"CasC":["Type I-E"],
"CasE":["Type I-E"],
"Cas12a":["Type V-A"],
"Cpf1":["Type V-A"],
"Cas12b":["Type V-B"],
"c2c1":["Type V-B"],
"Cas12c":["Type V-C"],
"c2c3":["Type V-C"],
"Cas12d":["Type V-D"],
"CasY":["Type V-D"],
"Cas12e":["Type V-E"],
"CasX":["Type V-E"],
"c2c4":["Type V-U1"],
"c2c5":["Type V-U5"],
"c2c8":["Type V-U2"],
"c2c10":["Type V-U3"],
"c2c9":["Type V-U4"],
"Cas13a":["Type VI-A"],
"c2c2":["Type VI-A"],
"Cas13b1":["Type VI-B1"],
"Cas13b2":["Type VI-B2"],
"c2c6":["Type VI-B1","Type VI-B2"],
"Csx27":["Type VI-B1"],
"Csx28":["Type VI-B2"],
"Cas13c":["Type VI-C"],
"c2c7":["Type VI-C"],
"Cas1":["Type I-A","Type I-B","Type I-C","Type I-U","Type I-D","Type I-E","Type I-F","Type I-G","Type II-A","Type II-B","Type II-C","Type III-A","Type III-B","Type V-A","Type V-B","Type V-C","Type V-D","Type V-E","Type VI-A"],
"Cas2":["Type I-A","Type I-B","Type I-C","Type I-U","Type I-D","Type I-E","Type I-F","Type I-G","Type II-A","Type II-B","Type II-C","Type III-A","Type III-B","Type V-A","Type V-B","Type V-E","Type VI-A"],
"Cas3":["Type I-A","Type I-B","Type I-C","Type I-U","Type I-D","Type I-E","Type I-F","Type I-G"],
"Cas3'":["Type I-A","Type I-D"],
"Cas3''":["Type I-A","Type I-D"],
}
Cas_synonym_list = {
"Csa1":"Cas4",
"Csa4":"Cas8a",
"Csx9":"Cas8a",
"Csh1":"Cas8b1",
"Csd1":"Cas8c",
"Csp2":"Cas8c",
"GSU0054":"Cas5",
"Csc3":"Cas10d",
"Csc2":"Cas7",
"Csc1":"Cas5",
"Cse1":"Cas8e",
"Cse3":"Cas6",
"Cse4":"Cas7",
"CasB":"Cse2",
"CasC":"Cas7",
"CasD":"Cas5",
"CasE":"Cas6",
"Csy1":"Cas8f",
"Csy2":"Cas5",
"Csy3":"Cas7",
"Csy4":"Cas6f",
"Cst1":"Cas8a1",
"Cst2":"Cas7",
"Cst5t":"Cas5",
"Csn1":"Cas9",
#skipping the Csm/Cmr proteins, as it is helpful to see them as is
"Csf4":"dinG",
"Csf2":"Cas7",
"Csf3":"Cas5",
"c2c2":"Cas13a",
"Cpf1":"Cas12a",
"c2c1":"Cas12b",
"c2c3":"Cas12c",
"CasY":"Cas12d",
"CasX":"Cas12e",
"c2c6":"Cas13b",
"c2c7":"Cas13c",
}
#According to Lange, et al. NAR, 2013: "CRISPRmap: an automated classification of repeat
#conservation in prokaryotic adaptive immune systems"
Repeat_families_to_types = {
"F1": ["I-B", "III-A", "III-B"],
"F2": ["I-E"],
"F3": ["I-C"],
"F4": ["I-C", "I-E", "II-B"],
"F5": ["I-F"],
"F6": ["I-A"],
"F7": ["I-A"],
"F8": ["I-F"],
"F9": ["III-B"],
"F10": ["I-B", "III-B"],
"F11": ["III-B"],
"F12": ["II-B", "III-A"],
"F13": ["I-A", "III-B"],
"F14": ["I-A", "I-D", "III-A"],
"F15": ["I-A", "III-B"],
"F16": ["III-A"],
"F17": ["?"],
"F18": ["I-E", "II-B"],
"F19": ["?"],
"F20": ["I-B"],
"F21": ["I-E"],
"F22": ["I-E"],
"F23": ["I-D", "II-B"],
"F24": ["III-A", "III-B"],
"F25": ["I-A", "II-B", "III-A"],
"F26": ["?"],
"F27": ["II-A", "II-B"],
"F28": ["I-A"],
"F29": ["III-A"],
"F30": ["?"],
"F31": ["III-A"],
"F32": ["I-C"],
"F33": ["I-C", "I-E", "II-B"],
"F34": ["II-B"],
"F35": ["II-A"],
"F36": ["?"],
"F37": ["I-C", "III-B"],
"F38": ["I-A", "III-B"],
"F39": ["I-A", "I-B", "II-B"],
"F40": ["I-B"],
"Cas12a_repeats": ["V-A"],
"Cas12b_repeats": ["V-B"],
"Cas12c_repeats": ["V-C"],
"Cas12d_repeats": ["V-D"],
"Cas12e_repeats": ["V-E"],
"Cas13a_repeats": ["VI-A"],
"Cas13b1_repeats": ["VI-B1"],
"Cas13b2_repeats": ["VI-B2"],
"Cas13c_repeats": ["VI-C"],
"c2c8_V-U2_repeats": ["V-U2"],
"c2c10_V-U3_repeats": ["V-U3"],
"c2c9_V-U4_repeats": ["V-U4"],
"c2c5_V-U5_repeats": ["V-U5"],
}
#Here, 1 means the Cas genes are expected to be upstream, while -1 is downstream (to be consistent with up_down), 0 means it is common to see both orientations
Expected_array_directions = {
"Type I-A":1,
"Type I-B":1,
"Type I-C":1,
"Type I-U":1,
"Type I-D":1,
"Type I-E":1,
"Type I-F":1,
"Type I-G":1,
"Type II-A":1,
"Type II-B":-1,
"Type II-C":-1,
"Type III-A":1,
"Type III-B":1,
"Type III-C":1,
"Type III-D":1,
"Type IV-A":1,
"Type V-A":1,
"Type V-B":1,
"Type V-C":1,
"Type V-D":1, #assumed
"Type V-E":1, #assumed
"Type V-U1":1, #assumed
"Type V-U2":1, #assumed
"Type V-U3":1, #assumed
"Type V-U4":1, #assumed
"Type V-U5":1, #assumed
"Type VI-A":1,
"Type VI-B1":1,
"Type VI-B2":1,
"Type VI-C":1,
"Type VI-D":1
}