Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Molecular Entropy for DNA or Amino Acid SequencesDescriptionEntropy (H) is a measure of uncertainty for a discrete random variable and is analogous to variation in continuous data. Traditionally the logarithm base for entropy is calculated with unit bits (b=2), nats (b=e) or dits (b=10). Alternatively, entropy estimates can be normalized to a common scale where 0<=H<=1 by setting b=n, the number of possible states. For DNA (n=4 nucleotide) or protein (n=20 amino acid) sequences, normalized entropy H=0 indicates an invariable site while H=1 represents a site where all states occur with equal probability. Atchley et al 1999 categorized amino acids according to physiochemical attributes to form (n=8) functional groups. In conjunction with the AA entropy, the GroupAA entropy value may provide insight to differences in functional and phylogenetic variation. AA Groups: acidic = DE aliphatic = AGILMV aminic = NQ aromatic = FWY basic = HKR cysteine = C hydroxylated = ST proline = P Gaps are ignored on a site by site basis so the entropy values may have different number of observations among sites. Sequences must be of the same length. UsageMolecularEntropy(x, type) Arguments
Value
Author(s)Lisa McFerrin ReferencesAtchley, W.R., Terhalle, W. and Dress, A. (1999) Positional dependence, cliques and predictive motifs in the bHLH protein domain. J. Mol. Evol. 48, 501-516 Kullback S. (1959) Information theory and statistics. Wiley, New York Examplesdata(bHLH288) bHLH_Seq = bHLH288[,2] MolecularEntropy(bHLH_Seq, "AA") MolecularEntropy(bHLH_Seq, "GroupAA") Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(HDMD)
Loading required package: psych
Loading required package: MASS
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HDMD/MolecularEntropy.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MolecularEntropy
> ### Title: Molecular Entropy for DNA or Amino Acid Sequences
> ### Aliases: MolecularEntropy
>
> ### ** Examples
>
>
> data(bHLH288)
Warning message:
In data(bHLH288) : data set 'bHLH288' not found
> bHLH_Seq = bHLH288[,2]
> MolecularEntropy(bHLH_Seq, "AA")
[1] "Warning: Data set contains non-Amino Acid elements"
$counts
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G 5 6 12 4 2 1 2 2 1 3 3 0 0 6
H 1 1 3 6 76 1 2 0 0 0 2 5 0 21
I 0 8 7 7 9 0 16 20 0 0 6 0 3 4
K 69 64 27 40 38 8 6 7 0 55 32 0 0 33
L 9 0 21 17 13 2 31 53 5 12 13 32 48 0
M 1 0 13 13 2 0 18 18 18 2 5 1 32 0
N 5 0 6 25 16 145 12 2 0 2 33 1 2 33
P 2 3 25 12 2 33 1 24 4 0 2 0 0 0
Q 13 4 7 6 3 1 6 11 0 2 37 0 18 32
R 149 174 33 7 3 19 5 103 0 187 85 233 134 20
S 3 3 24 20 20 10 11 2 5 16 10 1 0 17
T 2 9 12 35 13 22 8 3 2 5 7 0 12 2
V 1 0 32 14 5 2 28 13 2 0 12 0 37 1
W 0 2 1 2 0 0 0 1 0 0 8 0 0 0
Y 9 1 1 2 3 0 2 0 0 0 5 6 0 21
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S 22 0 13 35 50 0 54 9 0 13 15 9 0
T 4 1 8 14 0 0 10 24 0 1 17 2 19
V 2 46 0 6 9 0 9 3 3 0 3 23 106
W 0 0 0 0 5 0 0 0 0 0 0 1 0
Y 0 0 0 2 13 48 13 0 0 0 0 2 0
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L 20 37 58 18 1 3 0 152 0 0 35 13 9
M 2 2 3 10 0 3 0 11 0 0 17 2 3
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T 6 63 10 8 16 25 1 3 30 5 1 14 63
V 11 1 22 14 11 6 0 31 0 0 96 29 28
W 0 3 4 4 0 0 0 5 0 0 1 0 0
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C 0 0 2 0 7 3 4 2 1 2 0
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I 6 0 6 0 91 2 1 201 3 2 11
K 0 48 52 0 12 23 1 0 31 18 5
L 268 5 74 0 8 2 1 51 54 7 215
M 11 0 32 0 8 1 1 11 3 12 16
N 0 4 14 0 0 25 0 0 9 12 1
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R 0 106 11 0 7 26 2 0 61 10 15
S 0 8 16 15 5 44 0 0 8 53 1
T 0 5 1 49 44 8 0 1 2 10 0
V 3 1 2 46 83 3 14 20 0 6 8
W 0 0 0 0 0 0 0 0 21 1 0
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$H
[1] 0.54259103 0.44883025 0.89090476 0.84452658 0.73159258 0.58814523
[7] 0.80581970 0.68842679 0.30343823 0.39552039 0.78921575 0.24862201
[13] 0.53058028 0.83901329 0.75605248 0.54445120 0.29267861 0.79649265
[19] 0.66141578 0.42816934 0.80558916 0.71555892 0.02703858 0.46609526
[25] 0.75256327 0.67780158 0.50486094 0.37247846 0.84418416 0.87541708
[31] 0.83007461 0.75547989 0.72573297 0.42963784 0.53763591 0.55703509
[37] 0.13229774 0.63502436 0.66488249 0.33354940 0.10677790 0.60162860
[43] 0.74506712 0.34903553 0.62899873 0.74030411 0.34102393 0.31918223
[49] 0.79573864 0.86153174 0.36257321
> MolecularEntropy(bHLH_Seq, "GroupAA")
[1] "Warning: Data set contains non-Amino Acid elements"
$counts
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
acidic 5 8 34 5 9 36 87 6 222 1 6 1
aliphatic 25 18 111 118 102 10 146 129 54 19 44 33
aminic 18 4 13 31 19 146 18 13 0 4 70 1
aromatic 10 4 3 12 6 0 3 1 1 0 13 14
basic 219 239 63 53 117 28 13 110 0 242 119 238
cysteine 4 0 3 2 0 3 1 0 0 1 17 0
hydroxylated 5 12 36 55 33 32 19 5 7 21 17 1
proline 2 3 25 12 2 33 1 24 4 0 2 0
[,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23]
acidic 0 52 80 22 0 113 12 0 87 87 0
aliphatic 121 44 25 258 1 61 129 97 60 59 287
aminic 20 65 52 1 218 32 0 0 15 38 0
aromatic 0 25 0 6 0 3 19 191 33 0 0
basic 134 74 103 0 48 30 17 0 28 71 1
cysteine 1 8 2 0 0 0 61 0 1 0 0
hydroxylated 12 19 26 1 21 49 50 0 64 33 0
proline 0 0 0 0 0 0 0 0 0 0 0
[,24] [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34]
acidic 0 108 11 0 4 58 12 12 59 42 2
aliphatic 48 25 190 257 40 72 152 75 40 30 8
aminic 4 28 22 0 12 23 27 20 99 35 20
aromatic 0 0 3 0 1 16 23 24 4 1 0
basic 221 95 33 0 0 13 31 24 26 113 243
cysteine 0 0 18 12 3 8 8 7 7 0 0
hydroxylated 14 32 11 19 15 89 18 21 51 66 3
proline 1 0 0 0 213 9 17 105 2 1 12
[,35] [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45]
acidic 0 69 0 0 151 0 0 42 5 0 0
aliphatic 241 12 0 262 75 225 288 7 125 224 202
aminic 18 12 10 7 11 0 0 60 28 0 4
aromatic 6 0 0 6 0 0 0 1 7 0 1
basic 5 1 273 2 7 0 0 165 104 0 25
cysteine 0 0 0 4 0 0 0 0 2 0 7
hydroxylated 7 156 5 7 44 63 0 13 17 64 49
proline 11 38 0 0 0 0 0 0 0 0 0
[,46] [,47] [,48] [,49] [,50] [,51]
acidic 117 1 0 29 57 1
aliphatic 30 17 285 72 71 251
aminic 36 4 0 40 23 9
aromatic 0 231 0 29 35 0
basic 50 31 0 107 37 26
cysteine 3 4 2 1 2 0
hydroxylated 52 0 1 10 63 1
proline 0 0 0 0 0 0
$freq
[,1] [,2] [,3] [,4] [,5]
acidic 0.017361111 0.02777778 0.11805556 0.017361111 0.031250000
aliphatic 0.086805556 0.06250000 0.38541667 0.409722222 0.354166667
aminic 0.062500000 0.01388889 0.04513889 0.107638889 0.065972222
aromatic 0.034722222 0.01388889 0.01041667 0.041666667 0.020833333
basic 0.760416667 0.82986111 0.21875000 0.184027778 0.406250000
cysteine 0.013888889 0.00000000 0.01041667 0.006944444 0.000000000
hydroxylated 0.017361111 0.04166667 0.12500000 0.190972222 0.114583333
proline 0.006944444 0.01041667 0.08680556 0.041666667 0.006944444
[,6] [,7] [,8] [,9] [,10]
acidic 0.12500000 0.302083333 0.020833333 0.770833333 0.003472222
aliphatic 0.03472222 0.506944444 0.447916667 0.187500000 0.065972222
aminic 0.50694444 0.062500000 0.045138889 0.000000000 0.013888889
aromatic 0.00000000 0.010416667 0.003472222 0.003472222 0.000000000
basic 0.09722222 0.045138889 0.381944444 0.000000000 0.840277778
cysteine 0.01041667 0.003472222 0.000000000 0.000000000 0.003472222
hydroxylated 0.11111111 0.065972222 0.017361111 0.024305556 0.072916667
proline 0.11458333 0.003472222 0.083333333 0.013888889 0.000000000
[,11] [,12] [,13] [,14] [,15]
acidic 0.020833333 0.003472222 0.000000000 0.18118467 0.277777778
aliphatic 0.152777778 0.114583333 0.420138889 0.15331010 0.086805556
aminic 0.243055556 0.003472222 0.069444444 0.22648084 0.180555556
aromatic 0.045138889 0.048611111 0.000000000 0.08710801 0.000000000
basic 0.413194444 0.826388889 0.465277778 0.25783972 0.357638889
cysteine 0.059027778 0.000000000 0.003472222 0.02787456 0.006944444
hydroxylated 0.059027778 0.003472222 0.041666667 0.06620209 0.090277778
proline 0.006944444 0.000000000 0.000000000 0.00000000 0.000000000
[,16] [,17] [,18] [,19] [,20]
acidic 0.076388889 0.000000000 0.39236111 0.04166667 0.0000000
aliphatic 0.895833333 0.003472222 0.21180556 0.44791667 0.3368056
aminic 0.003472222 0.756944444 0.11111111 0.00000000 0.0000000
aromatic 0.020833333 0.000000000 0.01041667 0.06597222 0.6631944
basic 0.000000000 0.166666667 0.10416667 0.05902778 0.0000000
cysteine 0.000000000 0.000000000 0.00000000 0.21180556 0.0000000
hydroxylated 0.003472222 0.072916667 0.17013889 0.17361111 0.0000000
proline 0.000000000 0.000000000 0.00000000 0.00000000 0.0000000
[,21] [,22] [,23] [,24] [,25]
acidic 0.302083333 0.3020833 0.000000000 0.000000000 0.37500000
aliphatic 0.208333333 0.2048611 0.996527778 0.166666667 0.08680556
aminic 0.052083333 0.1319444 0.000000000 0.013888889 0.09722222
aromatic 0.114583333 0.0000000 0.000000000 0.000000000 0.00000000
basic 0.097222222 0.2465278 0.003472222 0.767361111 0.32986111
cysteine 0.003472222 0.0000000 0.000000000 0.000000000 0.00000000
hydroxylated 0.222222222 0.1145833 0.000000000 0.048611111 0.11111111
proline 0.000000000 0.0000000 0.000000000 0.003472222 0.00000000
[,26] [,27] [,28] [,29] [,30] [,31]
acidic 0.03819444 0.00000000 0.013888889 0.20138889 0.04166667 0.04166667
aliphatic 0.65972222 0.89236111 0.138888889 0.25000000 0.52777778 0.26041667
aminic 0.07638889 0.00000000 0.041666667 0.07986111 0.09375000 0.06944444
aromatic 0.01041667 0.00000000 0.003472222 0.05555556 0.07986111 0.08333333
basic 0.11458333 0.00000000 0.000000000 0.04513889 0.10763889 0.08333333
cysteine 0.06250000 0.04166667 0.010416667 0.02777778 0.02777778 0.02430556
hydroxylated 0.03819444 0.06597222 0.052083333 0.30902778 0.06250000 0.07291667
proline 0.00000000 0.00000000 0.739583333 0.03125000 0.05902778 0.36458333
[,32] [,33] [,34] [,35] [,36]
acidic 0.204861111 0.145833333 0.006944444 0.00000000 0.239583333
aliphatic 0.138888889 0.104166667 0.027777778 0.83680556 0.041666667
aminic 0.343750000 0.121527778 0.069444444 0.06250000 0.041666667
aromatic 0.013888889 0.003472222 0.000000000 0.02083333 0.000000000
basic 0.090277778 0.392361111 0.843750000 0.01736111 0.003472222
cysteine 0.024305556 0.000000000 0.000000000 0.00000000 0.000000000
hydroxylated 0.177083333 0.229166667 0.010416667 0.02430556 0.541666667
proline 0.006944444 0.003472222 0.041666667 0.03819444 0.131944444
[,37] [,38] [,39] [,40] [,41] [,42]
acidic 0.00000000 0.000000000 0.52430556 0.00000 0 0.145833333
aliphatic 0.00000000 0.909722222 0.26041667 0.78125 1 0.024305556
aminic 0.03472222 0.024305556 0.03819444 0.00000 0 0.208333333
aromatic 0.00000000 0.020833333 0.00000000 0.00000 0 0.003472222
basic 0.94791667 0.006944444 0.02430556 0.00000 0 0.572916667
cysteine 0.00000000 0.013888889 0.00000000 0.00000 0 0.000000000
hydroxylated 0.01736111 0.024305556 0.15277778 0.21875 0 0.045138889
proline 0.00000000 0.000000000 0.00000000 0.00000 0 0.000000000
[,43] [,44] [,45] [,46] [,47]
acidic 0.017361111 0.0000000 0.000000000 0.40625000
|
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and