cobot-tools-0.1.2.2: src/Bio/Tools/Sequence/CodonOptimization/Constants.hs
module Bio.Tools.Sequence.CodonOptimization.Constants
( ak2Codon
, codon2ak
, codonFrequencies
, ak2MaxFrequCodon
, motiveScoreWindow
, forbiddenMotiveScore
, defaultMotiveScore
) where
import Bio.NucleicAcid.Nucleotide.Type (DNA (..))
import Bio.Protein.AminoAcid.Type (AA (..))
import Bio.Tools.Sequence.CodonOptimization.Types (Organism (..))
import Data.Map as Map (Map,
fromList)
motiveScoreWindow :: Int
motiveScoreWindow = 100
forbiddenMotiveScore :: Double
forbiddenMotiveScore = 50
defaultMotiveScore :: Double
defaultMotiveScore = 0
ak2Codon :: Map AA [[DNA]]
ak2Codon =
fromList
[ (PHE, [[DT, DT, DT], [DT, DT, DC]])
, (TYR, [[DT, DA, DT], [DT, DA, DC]])
, (CYS, [[DT, DG, DT], [DT, DG, DC]])
, (TRP, [[DT, DG, DG]])
, (LEU, [[DT, DT, DA], [DT, DT, DG], [DC, DT, DT], [DC, DT, DC], [DC, DT, DA], [DC, DT, DG]])
, (PRO, [[DC, DC, DT], [DC, DC, DC], [DC, DC, DA], [DC, DC, DG]])
, (HIS, [[DC, DA, DT], [DC, DA, DC]])
, (GLN, [[DC, DA, DA], [DC, DA, DG]])
, (ILE, [[DA, DT, DT], [DA, DT, DC], [DA, DT, DA]])
, (MET, [[DA, DT, DG]])
, (THR, [[DA, DC, DT], [DA, DC, DC], [DA, DC, DA], [DA, DC, DG]])
, (ASN, [[DA, DA, DT], [DA, DA, DC]])
, (LYS, [[DA, DA, DA], [DA, DA, DG]])
, (SER, [[DT, DC, DT], [DT, DC, DC], [DT, DC, DA], [DT, DC, DG], [DA, DG, DT], [DA, DG, DC]])
, (ARG, [[DC, DG, DT], [DC, DG, DC], [DC, DG, DA], [DC, DG, DG], [DA, DG, DA], [DA, DG, DG]])
, (VAL, [[DG, DT, DT], [DG, DT, DC], [DG, DT, DA], [DG, DT, DG]])
, (ALA, [[DG, DC, DT], [DG, DC, DC], [DG, DC, DA], [DG, DC, DG]])
, (ASP, [[DG, DA, DT], [DG, DA, DC]])
, (GLU, [[DG, DA, DA], [DG, DA, DG]])
, (GLY, [[DG, DG, DT], [DG, DG, DC], [DG, DG, DA], [DG, DG, DG]])
]
codon2ak :: Map [DNA] AA
codon2ak =
fromList
[ ([DT, DT, DT], PHE)
, ([DT, DT, DC], PHE)
, ([DT, DT, DA], LEU)
, ([DT, DT, DG], LEU)
, ([DT, DC, DT], SER)
, ([DT, DC, DC], SER)
, ([DT, DC, DA], SER)
, ([DT, DC, DG], SER)
, ([DT, DA, DT], TYR)
, ([DT, DA, DC], TYR)
, ([DT, DG, DT], CYS)
, ([DT, DG, DC], CYS)
, ([DT, DG, DG], TRP)
, ([DC, DT, DT], LEU)
, ([DC, DT, DC], LEU)
, ([DC, DT, DA], LEU)
, ([DC, DT, DG], LEU)
, ([DC, DC, DT], PRO)
, ([DC, DC, DC], PRO)
, ([DC, DC, DA], PRO)
, ([DC, DC, DG], PRO)
, ([DC, DA, DT], HIS)
, ([DC, DA, DC], HIS)
, ([DC, DA, DA], GLN)
, ([DC, DA, DG], GLN)
, ([DC, DG, DT], ARG)
, ([DC, DG, DC], ARG)
, ([DC, DG, DA], ARG)
, ([DC, DG, DG], ARG)
, ([DA, DT, DT], ILE)
, ([DA, DT, DC], ILE)
, ([DA, DT, DA], ILE)
, ([DA, DT, DG], MET)
, ([DA, DC, DT], THR)
, ([DA, DC, DC], THR)
, ([DA, DC, DA], THR)
, ([DA, DC, DG], THR)
, ([DA, DA, DT], ASN)
, ([DA, DA, DC], ASN)
, ([DA, DA, DA], LYS)
, ([DA, DA, DG], LYS)
, ([DA, DG, DT], SER)
, ([DA, DG, DC], SER)
, ([DA, DG, DA], ARG)
, ([DA, DG, DG], ARG)
, ([DG, DT, DT], VAL)
, ([DG, DT, DC], VAL)
, ([DG, DT, DA], VAL)
, ([DG, DT, DG], VAL)
, ([DG, DC, DT], ALA)
, ([DG, DC, DC], ALA)
, ([DG, DC, DA], ALA)
, ([DG, DC, DG], ALA)
, ([DG, DA, DT], ASP)
, ([DG, DA, DC], ASP)
, ([DG, DA, DA], GLU)
, ([DG, DA, DG], GLU)
, ([DG, DG, DT], GLY)
, ([DG, DG, DC], GLY)
, ([DG, DG, DA], GLY)
, ([DG, DG, DG], GLY)
]
ak2MaxFrequCodon :: Organism -> Map AA ([DNA], Double)
-- taken from https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/blob/master/codon_usage_data/tables/h_sapiens_9606.csv
ak2MaxFrequCodon Human =
fromList
[ (ALA, ([DG, DC, DC], 0.4))
, (CYS, ([DT, DG, DC], 0.54))
, (ASP, ([DG, DA, DC], 0.54))
, (GLU, ([DG, DA, DG], 0.58))
, (PHE, ([DT, DT, DC], 0.54))
, (GLY, ([DG, DG, DC], 0.34))
, (HIS, ([DC, DA, DC], 0.58))
, (ILE, ([DA, DT, DC], 0.47))
, (LYS, ([DA, DA, DG], 0.57))
, (LEU, ([DC, DT, DG], 0.4))
, (MET, ([DA, DT, DG], 1.0))
, (ASN, ([DA, DA, DC], 0.53))
, (PRO, ([DC, DC, DC], 0.32))
, (GLN, ([DC, DA, DG], 0.73))
, (ARG, ([DA, DG, DG], 0.21))
, (SER, ([DA, DG, DC], 0.24))
, (THR, ([DA, DC, DC], 0.36))
, (VAL, ([DG, DT, DG], 0.46))
, (TRP, ([DT, DG, DG], 1.0))
, (TYR, ([DT, DA, DC], 0.56))
]
-- taken from https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/blob/master/codon_usage_data/tables/e_coli_316407.csv
ak2MaxFrequCodon EColi =
fromList
[ (ALA, ([DG, DC, DG], 0.36))
, (CYS, ([DT, DG, DC], 0.56))
, (ASP, ([DG, DA, DT], 0.63))
, (GLU, ([DG, DA, DA], 0.68))
, (PHE, ([DT, DT, DT], 0.58))
, (GLY, ([DG, DG, DC], 0.41))
, (HIS, ([DC, DA, DT], 0.57))
, (ILE, ([DA, DT, DT], 0.51))
, (LYS, ([DA, DA, DA], 0.76))
, (LEU, ([DC, DT, DG], 0.50))
, (MET, ([DA, DT, DG], 1.0))
, (ASN, ([DA, DA, DC], 0.55))
, (PRO, ([DC, DC, DG], 0.53))
, (GLN, ([DC, DA, DG], 0.65))
, (ARG, ([DC, DG, DC], 0.4))
, (SER, ([DA, DG, DC], 0.28))
, (THR, ([DA, DC, DC], 0.44))
, (VAL, ([DG, DT, DG], 0.37))
, (TRP, ([DT, DG, DG], 1.0))
, (TYR, ([DT, DA, DT], 0.57))
]
-- taken from https://www.genscript.com/tools/codon-frequency-table
ak2MaxFrequCodon CHO =
fromList
[ (ALA, ([DG, DC, DC], 0.37))
, (CYS, ([DT, DG, DC], 0.53))
, (ASP, ([DG, DA, DC], 0.53))
, (GLU, ([DG, DA, DG], 0.59))
, (PHE, ([DT, DT, DC], 0.53))
, (GLY, ([DG, DG, DC], 0.34))
, (HIS, ([DC, DA, DC], 0.56))
, (ILE, ([DA, DT, DC], 0.51))
, (LYS, ([DA, DA, DG], 0.61))
, (LEU, ([DC, DT, DG], 0.39))
, (MET, ([DA, DT, DG], 1.0))
, (ASN, ([DA, DA, DC], 0.55))
, (PRO, ([DC, DC, DC], 0.32))
, (GLN, ([DC, DA, DG], 0.76))
, (ARG, ([DC, DG, DG], 0.19))
, (SER, ([DA, DG, DC], 0.22))
, (THR, ([DA, DC, DC], 0.37))
, (VAL, ([DG, DT, DG], 0.46))
, (TRP, ([DT, DG, DG], 1.0))
, (TYR, ([DT, DA, DC], 0.56))
]
codonFrequencies :: Organism -> Map [DNA] Double
-- taken from https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/blob/master/codon_usage_data/tables/h_sapiens_9606.csv
codonFrequencies Human =
fromList
[ ([DT, DA, DA], 0.30)
, ([DT, DA, DG], 0.24)
, ([DT, DG, DA], 0.47)
, ([DG, DC, DA], 0.23)
, ([DG, DC, DC], 0.40)
, ([DG, DC, DG], 0.11)
, ([DG, DC, DT], 0.27)
, ([DT, DG, DC], 0.54)
, ([DT, DG, DT], 0.46)
, ([DG, DA, DC], 0.54)
, ([DG, DA, DT], 0.46)
, ([DG, DA, DA], 0.42)
, ([DG, DA, DG], 0.58)
, ([DT, DT, DC], 0.54)
, ([DT, DT, DT], 0.46)
, ([DG, DG, DA], 0.25)
, ([DG, DG, DC], 0.34)
, ([DG, DG, DG], 0.25)
, ([DG, DG, DT], 0.16)
, ([DC, DA, DC], 0.58)
, ([DC, DA, DT], 0.42)
, ([DA, DT, DA], 0.17)
, ([DA, DT, DC], 0.47)
, ([DA, DT, DT], 0.36)
, ([DA, DA, DA], 0.43)
, ([DA, DA, DG], 0.57)
, ([DC, DT, DA], 0.07)
, ([DC, DT, DC], 0.20)
, ([DC, DT, DG], 0.40)
, ([DC, DT, DT], 0.13)
, ([DT, DT, DA], 0.08)
, ([DT, DT, DG], 0.13)
, ([DA, DT, DG], 1.00)
, ([DA, DA, DC], 0.53)
, ([DA, DA, DT], 0.47)
, ([DC, DC, DA], 0.28)
, ([DC, DC, DC], 0.32)
, ([DC, DC, DG], 0.11)
, ([DC, DC, DT], 0.29)
, ([DC, DA, DA], 0.27)
, ([DC, DA, DG], 0.73)
, ([DA, DG, DA], 0.21)
, ([DA, DG, DG], 0.21)
, ([DC, DG, DA], 0.11)
, ([DC, DG, DC], 0.18)
, ([DC, DG, DG], 0.20)
, ([DC, DG, DT], 0.08)
, ([DA, DG, DC], 0.24)
, ([DA, DG, DT], 0.15)
, ([DT, DC, DA], 0.15)
, ([DT, DC, DC], 0.22)
, ([DT, DC, DG], 0.05)
, ([DT, DC, DT], 0.19)
, ([DA, DC, DA], 0.28)
, ([DA, DC, DC], 0.36)
, ([DA, DC, DG], 0.11)
, ([DA, DC, DT], 0.25)
, ([DG, DT, DA], 0.12)
, ([DG, DT, DC], 0.24)
, ([DG, DT, DG], 0.46)
, ([DG, DT, DT], 0.18)
, ([DT, DG, DG], 1.00)
, ([DT, DA, DC], 0.56)
, ([DT, DA, DT], 0.44)
]
-- taken from https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/blob/master/codon_usage_data/tables/e_coli_316407.csv
codonFrequencies EColi =
fromList
[ ([DG, DC, DA], 0.21)
, ([DG, DC, DC], 0.27)
, ([DG, DC, DG], 0.36)
, ([DG, DC, DT], 0.16)
, ([DT, DG, DC], 0.56)
, ([DT, DG, DT], 0.44)
, ([DG, DA, DC], 0.37)
, ([DG, DA, DT], 0.63)
, ([DG, DA, DA], 0.69)
, ([DG, DA, DG], 0.31)
, ([DT, DT, DC], 0.43)
, ([DT, DT, DT], 0.57)
, ([DG, DG, DA], 0.11)
, ([DG, DG, DC], 0.41)
, ([DG, DG, DG], 0.15)
, ([DG, DG, DT], 0.34)
, ([DC, DA, DC], 0.43)
, ([DC, DA, DT], 0.57)
, ([DA, DT, DA], 0.07)
, ([DA, DT, DC], 0.42)
, ([DA, DT, DT], 0.51)
, ([DA, DA, DA], 0.76)
, ([DA, DA, DG], 0.24)
, ([DC, DT, DA], 0.04)
, ([DC, DT, DC], 0.10)
, ([DC, DT, DG], 0.50)
, ([DC, DT, DT], 0.10)
, ([DT, DT, DA], 0.13)
, ([DT, DT, DG], 0.13)
, ([DA, DT, DG], 1.00)
, ([DA, DA, DC], 0.55)
, ([DA, DA, DT], 0.45)
, ([DC, DC, DA], 0.19)
, ([DC, DC, DC], 0.12)
, ([DC, DC, DG], 0.53)
, ([DC, DC, DT], 0.16)
, ([DC, DA, DA], 0.35)
, ([DC, DA, DG], 0.65)
, ([DA, DG, DA], 0.04)
, ([DA, DG, DG], 0.02)
, ([DC, DG, DA], 0.06)
, ([DC, DG, DC], 0.40)
, ([DC, DG, DG], 0.10)
, ([DC, DG, DT], 0.38)
, ([DA, DG, DC], 0.28)
, ([DA, DG, DT], 0.15)
, ([DT, DC, DA], 0.12)
, ([DT, DC, DC], 0.15)
, ([DT, DC, DG], 0.15)
, ([DT, DC, DT], 0.15)
, ([DA, DC, DA], 0.13)
, ([DA, DC, DC], 0.44)
, ([DA, DC, DG], 0.27)
, ([DA, DC, DT], 0.16)
, ([DG, DT, DA], 0.15)
, ([DG, DT, DC], 0.22)
, ([DG, DT, DG], 0.37)
, ([DG, DT, DT], 0.26)
, ([DT, DG, DG], 1.00)
, ([DT, DA, DC], 0.43)
, ([DT, DA, DT], 0.57)
]
-- taken from https://www.genscript.com/tools/codon-frequency-table
codonFrequencies CHO =
fromList
[ ([DT, DT, DT], 0.47)
, ([DT, DT, DC], 0.53)
, ([DT, DT, DA], 0.07)
, ([DT, DT, DG], 0.14)
, ([DT, DC, DT], 0.22)
, ([DT, DC, DC], 0.22)
, ([DT, DC, DA], 0.14)
, ([DT, DC, DG], 0.05)
, ([DT, DA, DT], 0.44)
, ([DT, DA, DC], 0.56)
, ([DT, DA, DA], 0.26)
, ([DT, DA, DG], 0.22)
, ([DT, DG, DT], 0.47)
, ([DT, DG, DC], 0.53)
, ([DT, DG, DA], 0.53)
, ([DT, DG, DG], 1.00)
, ([DC, DT, DT], 0.13)
, ([DC, DT, DC], 0.19)
, ([DC, DT, DA], 0.08)
, ([DC, DT, DG], 0.39)
, ([DC, DC, DT], 0.31)
, ([DC, DC, DC], 0.32)
, ([DC, DC, DA], 0.29)
, ([DC, DC, DG], 0.08)
, ([DC, DA, DT], 0.44)
, ([DC, DA, DC], 0.56)
, ([DC, DA, DA], 0.24)
, ([DC, DA, DG], 0.76)
, ([DC, DG, DT], 0.11)
, ([DC, DG, DC], 0.18)
, ([DC, DG, DA], 0.14)
, ([DC, DG, DG], 0.19)
, ([DA, DT, DT], 0.35)
, ([DA, DT, DC], 0.51)
, ([DA, DT, DA], 0.14)
, ([DA, DT, DG], 1.00)
, ([DA, DC, DT], 0.26)
, ([DA, DC, DC], 0.37)
, ([DA, DC, DA], 0.29)
, ([DA, DC, DG], 0.08)
, ([DA, DA, DT], 0.45)
, ([DA, DA, DC], 0.55)
, ([DA, DA, DA], 0.39)
, ([DA, DA, DG], 0.61)
, ([DA, DG, DT], 0.15)
, ([DA, DG, DC], 0.22)
, ([DA, DG, DA], 0.19)
, ([DA, DG, DG], 0.19)
, ([DG, DT, DT], 0.18)
, ([DG, DT, DC], 0.24)
, ([DG, DT, DA], 0.12)
, ([DG, DT, DG], 0.46)
, ([DG, DC, DT], 0.32)
, ([DG, DC, DC], 0.37)
, ([DG, DC, DA], 0.23)
, ([DG, DC, DG], 0.07)
, ([DG, DA, DT], 0.47)
, ([DG, DA, DC], 0.53)
, ([DG, DA, DA], 0.41)
, ([DG, DA, DG], 0.59)
, ([DG, DG, DT], 0.20)
, ([DG, DG, DC], 0.34)
, ([DG, DG, DA], 0.25)
, ([DG, DG, DG], 0.21)
]