aminoacyl: Codon usage
In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences
Description
Usage
Format
Source
References
Examples
Description
aminoacyl is a list containing the codon counts of 36 genes encoding yeast aminoacyl-tRNA-synthetase(S.Cerevisiae).
Usage
1
Format
aminoacyl is a list containing the 5 following objects:
- genes
is a vector giving the gene names.
- localisation
is a vector giving the cellular localisation
of the proteins (M = mitochondrial, C = cytoplasmic,
I = indetermined, CI = cyto and mito).
- codon
is a vector containing the 64 triplets.
- AA
is a factor giving the amino acid names for each codon.
- usage.codon
is a dataframe containing the codon counts for each gene.
Source
Data prepared by D. Charif Delphine.Charif@versailles.inra.fr starting from:
http://www.expasy.org/sprot/
References
Chiapello H., Olivier E., Landes-Devauchelle C., Nitschké P. and Risler J.L (1999)
Codon usage as a tool to predict the cellular localisation of eukariotic ribosomal
proteins and aminoacyl-tRNA synthetases. Nucleic Acids Res., 27, 14, 2848–2851.
Examples
1
2
3
4
Example output
[1] "YCR024C" "YDR268W" "YGR094W" "YGR171C" "YHR011W" "YHR091C" "YKL194C"
[8] "YLR382C" "YNL073W" "YOL033W" "YPL040C" "YPL097W" "YPL104W" "YPR033C"
[15] "YPR047W" "YNL247W" "YPR081C" "YBL076C" "YBR121C" "YDR023W" "YDR037W"
[22] "YDR341C" "YER087W" "YFL022C" "YGL245W" "YGR185C" "YGR264C" "YHR019C"
[29] "YIL078W" "YLR060W" "YOL097C" "YOR335C" "YPL160W" "YHR020W" "YOR168W"
[36] "YLL018C"
YCR024C YDR268W YGR094W YGR171C YHR011W YHR091C YKL194C YLR382C YNL073W
GCT 4 8 46 9 9 3 12 19 3
GCC 4 4 16 5 6 13 4 6 3
GCA 7 7 7 3 12 14 2 21 9
GCG 2 4 2 2 5 2 2 3 6
CGT 3 3 13 4 1 9 4 5 3
CGC 2 3 1 0 3 4 3 3 2
CGA 1 0 1 5 2 3 1 4 2
CGG 1 0 1 0 1 2 0 0 0
AGA 13 8 20 12 7 15 10 17 11
AGG 3 3 6 7 7 4 5 6 12
AAT 17 11 23 24 19 23 17 30 19
AAC 7 7 26 10 8 15 12 17 16
GAT 13 17 45 20 15 21 17 34 18
GAC 5 5 24 11 6 16 11 17 13
TGT 5 2 10 6 5 3 2 6 4
TGC 3 0 3 2 3 3 3 6 5
CAA 18 9 29 20 14 16 12 22 17
CAG 5 6 4 6 8 16 7 12 10
GAA 24 18 73 24 17 19 22 45 20
GAG 9 4 19 11 16 8 9 11 15
GGT 8 3 49 9 6 10 13 12 9
GGC 3 8 7 11 3 8 3 10 11
GGA 8 4 2 7 10 10 5 14 5
GGG 5 2 1 1 3 9 1 11 3
CAT 5 5 17 10 3 10 10 7 6
CAC 9 7 7 5 1 5 2 9 3
ATT 11 12 46 22 13 17 15 30 15
ATC 5 6 27 6 7 7 7 10 9
ATA 15 5 1 16 15 22 7 20 12
TTA 20 11 30 15 11 21 9 21 16
TTG 10 8 42 13 10 12 10 21 19
CTT 5 7 8 4 5 12 7 5 8
CTC 3 0 2 6 2 2 3 7 4
CTA 9 3 6 8 8 14 7 7 8
CTG 4 6 8 8 6 5 6 10 17
AAA 24 24 50 35 26 34 23 58 16
AAG 10 11 63 13 16 13 18 22 32
ATG 8 10 16 9 10 20 14 24 12
TTT 21 11 19 15 9 17 15 28 19
TTC 9 5 24 14 5 16 16 18 11
CCT 9 9 17 9 6 5 7 20 11
CCC 3 0 2 3 1 4 4 9 6
CCA 11 6 31 11 10 10 8 14 3
CCG 2 2 2 5 2 3 4 11 7
TCT 9 7 27 9 4 10 13 14 6
TCC 9 4 16 16 1 10 4 6 9
TCA 14 3 6 8 10 13 3 13 9
TCG 5 8 5 4 4 9 6 4 6
AGT 4 8 6 7 6 4 1 12 9
AGC 3 3 7 4 6 5 1 10 5
TAA 0 0 0 0 1 1 1 1 1
TAG 0 0 1 0 0 0 0 0 0
TGA 1 1 0 1 0 0 0 0 0
ACT 15 5 35 6 4 5 11 18 9
ACC 9 1 17 4 7 6 0 11 5
ACA 8 7 8 8 6 8 4 11 5
ACG 3 4 2 5 5 6 5 6 10
TGG 8 4 25 11 4 8 10 19 4
TAT 13 8 16 16 6 15 7 16 9
TAC 7 4 19 9 9 9 8 11 11
GTT 12 12 45 15 8 14 7 18 9
GTC 3 4 17 3 2 6 2 14 9
GTA 3 9 6 8 9 11 6 15 7
GTG 4 4 1 6 3 9 5 14 4
YOL033W YPL040C YPL097W YPL104W YPR033C YPR047W YNL247W YPR081C YBL076C
GCT 8 12 12 12 29 5 23 6 26
GCC 5 8 3 11 10 4 14 4 18
GCA 9 17 3 9 10 1 11 9 11
GCG 5 5 5 3 3 3 1 2 1
CGT 2 4 3 3 4 4 3 3 15
CGC 1 7 0 1 0 3 3 2 1
CGA 3 4 5 2 1 1 0 5 0
CGG 3 0 2 2 0 0 0 1 1
AGA 14 18 7 17 11 16 16 16 28
AGG 6 13 11 9 6 4 2 9 1
AAT 12 29 19 26 11 16 27 22 19
AAC 14 22 10 11 5 11 23 12 27
GAT 22 36 20 25 24 23 34 23 48
GAC 6 16 9 14 11 9 19 13 30
TGT 10 11 6 3 5 1 4 6 9
TGC 1 3 1 5 0 5 2 2 0
CAA 9 32 11 13 12 9 28 13 20
CAG 6 17 11 10 4 3 9 12 4
GAA 22 53 15 28 31 24 38 32 59
GAG 13 14 5 18 9 11 15 14 20
GGT 11 12 12 14 30 2 17 15 43
GGC 4 12 5 7 7 6 11 4 7
GGA 7 18 13 7 2 8 5 10 6
GGG 6 5 4 4 1 3 1 8 1
CAT 9 25 5 10 2 9 15 9 13
CAC 7 9 3 2 4 5 1 4 7
ATT 9 29 13 18 20 16 29 22 44
ATC 8 20 11 13 15 8 19 10 20
ATA 18 23 11 12 4 11 3 12 3
TTA 15 34 16 16 14 9 25 16 34
TTG 22 26 16 20 18 12 28 23 46
CTT 10 16 6 4 4 8 3 4 7
CTC 1 10 4 6 1 4 0 2 1
CTA 10 23 8 8 6 6 8 7 7
CTG 7 10 5 8 1 4 2 6 4
AAA 28 50 23 37 25 26 40 29 50
AAG 23 29 11 24 29 14 37 17 43
ATG 12 15 7 15 12 14 12 18 18
TTT 21 25 15 31 10 13 23 24 22
TTC 5 13 7 8 10 6 15 15 31
CCT 12 11 6 8 7 6 9 8 14
CCC 3 9 5 4 1 4 5 4 2
CCA 9 13 5 18 7 7 13 8 28
CCG 2 8 0 4 0 3 3 5 1
TCT 17 14 8 11 21 9 14 5 26
TCC 3 15 6 6 8 4 16 7 21
TCA 6 20 11 9 9 14 9 10 12
TCG 6 6 4 4 2 0 4 11 1
AGT 3 11 11 12 5 3 6 6 8
AGC 4 13 3 3 1 3 5 1 3
TAA 1 0 1 0 1 0 0 1 0
TAG 0 0 0 0 0 1 1 0 0
TGA 0 1 0 1 0 0 0 0 1
ACT 5 17 9 7 14 9 19 16 25
ACC 7 11 1 8 5 7 11 5 17
ACA 5 16 9 10 7 9 8 10 12
ACG 7 8 6 5 2 4 5 7 4
TGG 5 18 3 5 4 10 14 6 22
TAT 15 25 12 13 10 10 9 5 25
TAC 5 17 7 9 7 5 12 8 22
GTT 6 19 9 12 19 10 19 10 44
GTC 6 9 4 5 10 4 9 6 24
GTA 4 8 10 8 2 11 3 9 5
GTG 2 9 10 11 4 5 8 10 11
YBR121C YDR023W YDR037W YDR341C YER087W YFL022C YGL245W YGR185C YGR264C
GCT 25 16 21 18 10 10 35 11 22
GCC 17 6 14 10 3 12 13 9 11
GCA 7 1 1 11 6 4 3 6 13
GCG 0 1 1 4 5 1 1 5 1
CGT 5 4 9 7 4 4 10 0 10
CGC 2 0 1 1 2 0 0 0 1
CGA 0 0 0 0 3 0 0 0 0
CGG 0 0 0 0 1 0 0 0 0
AGA 26 12 23 19 12 15 23 8 12
AGG 3 1 2 1 6 0 3 2 1
AAT 13 11 10 13 24 9 15 9 30
AAC 10 12 11 13 11 17 21 12 24
GAT 29 17 24 22 31 15 43 10 30
GAC 20 7 17 12 10 20 21 8 15
TGT 6 5 8 2 11 1 6 3 10
TGC 0 3 1 1 4 0 1 1 0
CAA 15 17 24 20 11 20 16 15 24
CAG 1 4 2 4 11 5 0 2 3
GAA 52 40 46 36 27 26 44 23 44
GAG 9 11 9 14 10 12 2 7 7
GGT 30 21 29 28 14 21 24 17 29
GGC 5 2 2 7 8 2 6 4 2
GGA 4 3 1 3 11 1 6 1 5
GGG 2 0 1 0 3 4 1 1 1
CAT 12 5 7 7 8 4 4 3 17
CAC 3 4 9 7 5 8 10 2 5
ATT 21 12 17 22 13 9 28 9 23
ATC 14 13 10 18 11 17 18 12 15
ATA 2 1 1 1 14 1 4 0 3
TTA 18 17 12 24 17 7 19 10 22
TTG 32 17 27 18 15 23 32 19 34
CTT 3 2 5 6 5 9 1 4 4
CTC 0 1 1 1 2 4 1 2 1
CTA 2 4 5 6 6 7 7 5 8
CTG 1 0 2 6 11 8 1 1 6
AAA 30 24 23 29 35 20 27 21 34
AAG 30 26 25 22 15 21 49 21 28
ATG 12 6 20 19 16 14 17 9 10
TTT 22 7 13 15 18 7 8 12 18
TTC 11 13 17 14 5 19 21 8 14
CCT 7 3 7 5 6 8 8 6 9
CCC 0 1 0 3 4 4 2 2 1
CCA 23 15 23 11 9 8 20 17 24
CCG 0 0 3 1 1 0 0 1 0
TCT 19 12 11 15 5 11 13 5 22
TCC 11 10 7 5 4 12 6 5 7
TCA 4 3 3 5 14 3 5 3 10
TCG 0 0 1 3 6 4 1 1 5
AGT 5 3 0 1 11 0 2 3 7
AGC 0 1 1 2 5 1 3 2 3
TAA 1 1 1 1 0 1 1 1 1
TAG 0 0 0 0 1 0 0 0 0
TGA 0 0 0 0 0 0 0 0 0
ACT 13 7 12 11 8 5 20 5 11
ACC 9 4 10 5 4 16 13 8 2
ACA 4 1 7 8 8 6 2 2 12
ACG 2 1 0 1 2 3 2 2 7
TGG 7 6 2 9 10 6 12 1 13
TAT 10 8 7 13 8 3 8 7 20
TAC 8 13 13 11 10 12 15 6 15
GTT 33 15 15 24 10 9 22 14 32
GTC 17 8 14 8 7 12 22 8 7
GTA 1 4 3 3 6 0 1 1 1
GTG 0 1 1 2 4 3 6 3 6
YHR019C YIL078W YLR060W YOL097C YOR335C YPL160W YHR020W YOR168W YLL018C
GCT 20 17 16 6 39 43 25 20 21
GCC 12 17 16 7 19 24 17 7 14
GCA 9 3 3 7 8 24 7 15 8
GCG 0 2 2 2 2 6 0 6 0
CGT 9 10 7 4 12 15 5 3 10
CGC 1 0 0 1 1 1 2 0 1
CGA 0 0 0 0 0 0 0 0 0
CGG 0 0 0 0 0 0 0 0 0
AGA 17 27 17 10 20 20 26 14 19
AGG 0 2 1 1 2 5 3 5 6
AAT 4 12 14 7 27 18 13 15 4
AAC 8 20 18 4 23 21 10 12 12
GAT 11 30 22 20 49 50 29 16 10
GAC 26 14 18 15 24 14 20 9 23
TGT 8 9 8 5 6 11 6 7 3
TGC 1 3 1 1 1 2 0 2 0
CAA 20 23 15 19 23 31 15 14 18
CAG 4 4 3 3 3 6 1 1 5
GAA 34 56 31 22 66 81 52 29 43
GAG 10 8 16 6 12 18 9 8 14
GGT 27 31 18 17 60 42 30 17 27
GGC 6 5 6 4 10 9 5 3 1
GGA 3 6 0 2 3 3 4 13 0
GGG 1 5 4 2 3 6 2 3 4
CAT 8 13 7 7 11 12 12 9 4
CAC 2 6 8 2 5 8 3 5 8
ATT 13 21 20 11 29 46 21 24 16
ATC 14 13 19 6 24 22 14 11 12
ATA 1 1 4 2 3 6 2 9 0
TTA 7 21 15 7 20 28 18 13 6
TTG 35 31 25 16 38 30 32 21 36
CTT 1 1 5 3 8 5 3 8 3
CTC 2 0 0 0 1 1 0 1 2
CTA 5 6 8 4 6 9 2 9 7
CTG 4 3 2 3 6 4 1 4 2
AAA 13 32 23 18 39 47 30 24 16
AAG 30 33 23 26 52 53 30 15 32
ATG 11 22 13 8 10 27 12 16 11
TTT 7 18 13 16 26 30 22 10 12
TTC 15 21 16 19 27 29 11 5 16
CCT 3 4 7 7 11 19 7 11 7
CCC 2 0 0 1 4 1 0 3 5
CCA 17 22 21 12 22 29 23 15 14
CCG 0 2 2 1 1 3 0 3 0
TCT 13 28 11 3 25 28 19 16 7
TCC 13 7 13 9 11 6 11 9 10
TCA 3 3 5 4 8 12 4 6 2
TCG 1 2 4 2 1 2 0 1 1
AGT 2 6 2 1 3 3 5 5 5
AGC 3 1 3 5 2 5 0 2 3
TAA 0 1 1 1 1 1 1 1 0
TAG 0 0 0 0 0 0 0 0 0
TGA 1 0 0 0 0 0 0 0 1
ACT 12 18 9 9 26 23 13 9 5
ACC 17 10 14 10 13 15 9 4 13
ACA 5 2 4 6 8 13 4 12 6
ACG 2 0 3 2 1 6 2 6 1
TGG 4 13 4 3 8 13 7 1 1
TAT 10 8 4 3 13 26 10 9 6
TAC 13 16 13 9 22 26 8 7 12
GTT 13 24 17 12 36 25 33 18 11
GTC 15 18 12 8 16 17 17 11 11
GTA 4 3 6 5 3 8 1 10 4
GTG 3 1 4 7 6 3 0 10 7
Duality diagramm
class: coa dudi
$call: dudi.coa(df = aminoacyl$usage.codon, scannf = FALSE)
$nf: 2 axis-components saved
$rank: 34
eigen values: 0.07774 0.01301 0.008387 0.007261 0.006383 ...
vector length mode content
1 $cw 36 numeric column weights
2 $lw 64 numeric row weights
3 $eig 34 numeric eigen values
data.frame nrow ncol content
1 $tab 64 36 modified array
2 $li 64 2 row coordinates
3 $l1 64 2 row normed scores
4 $co 36 2 column coordinates
5 $c1 36 2 column normed scores
other elements: N
ade4 documentation built on May 2, 2019, 5:50 p.m.
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Description Usage Format Source References Examples
Description
aminoacyl is a list containing the codon counts of 36 genes encoding yeast aminoacyl-tRNA-synthetase(S.Cerevisiae).
Usage
1 |
Format
aminoacyl is a list containing the 5 following objects:
- genes
is a vector giving the gene names.
- localisation
is a vector giving the cellular localisation of the proteins (M = mitochondrial, C = cytoplasmic, I = indetermined, CI = cyto and mito).
- codon
is a vector containing the 64 triplets.
- AA
is a factor giving the amino acid names for each codon.
- usage.codon
is a dataframe containing the codon counts for each gene.
Source
Data prepared by D. Charif Delphine.Charif@versailles.inra.fr starting from:
http://www.expasy.org/sprot/
References
Chiapello H., Olivier E., Landes-Devauchelle C., Nitschké P. and Risler J.L (1999) Codon usage as a tool to predict the cellular localisation of eukariotic ribosomal proteins and aminoacyl-tRNA synthetases. Nucleic Acids Res., 27, 14, 2848–2851.
Examples
1 2 3 4 |
Example output
[1] "YCR024C" "YDR268W" "YGR094W" "YGR171C" "YHR011W" "YHR091C" "YKL194C"
[8] "YLR382C" "YNL073W" "YOL033W" "YPL040C" "YPL097W" "YPL104W" "YPR033C"
[15] "YPR047W" "YNL247W" "YPR081C" "YBL076C" "YBR121C" "YDR023W" "YDR037W"
[22] "YDR341C" "YER087W" "YFL022C" "YGL245W" "YGR185C" "YGR264C" "YHR019C"
[29] "YIL078W" "YLR060W" "YOL097C" "YOR335C" "YPL160W" "YHR020W" "YOR168W"
[36] "YLL018C"
YCR024C YDR268W YGR094W YGR171C YHR011W YHR091C YKL194C YLR382C YNL073W
GCT 4 8 46 9 9 3 12 19 3
GCC 4 4 16 5 6 13 4 6 3
GCA 7 7 7 3 12 14 2 21 9
GCG 2 4 2 2 5 2 2 3 6
CGT 3 3 13 4 1 9 4 5 3
CGC 2 3 1 0 3 4 3 3 2
CGA 1 0 1 5 2 3 1 4 2
CGG 1 0 1 0 1 2 0 0 0
AGA 13 8 20 12 7 15 10 17 11
AGG 3 3 6 7 7 4 5 6 12
AAT 17 11 23 24 19 23 17 30 19
AAC 7 7 26 10 8 15 12 17 16
GAT 13 17 45 20 15 21 17 34 18
GAC 5 5 24 11 6 16 11 17 13
TGT 5 2 10 6 5 3 2 6 4
TGC 3 0 3 2 3 3 3 6 5
CAA 18 9 29 20 14 16 12 22 17
CAG 5 6 4 6 8 16 7 12 10
GAA 24 18 73 24 17 19 22 45 20
GAG 9 4 19 11 16 8 9 11 15
GGT 8 3 49 9 6 10 13 12 9
GGC 3 8 7 11 3 8 3 10 11
GGA 8 4 2 7 10 10 5 14 5
GGG 5 2 1 1 3 9 1 11 3
CAT 5 5 17 10 3 10 10 7 6
CAC 9 7 7 5 1 5 2 9 3
ATT 11 12 46 22 13 17 15 30 15
ATC 5 6 27 6 7 7 7 10 9
ATA 15 5 1 16 15 22 7 20 12
TTA 20 11 30 15 11 21 9 21 16
TTG 10 8 42 13 10 12 10 21 19
CTT 5 7 8 4 5 12 7 5 8
CTC 3 0 2 6 2 2 3 7 4
CTA 9 3 6 8 8 14 7 7 8
CTG 4 6 8 8 6 5 6 10 17
AAA 24 24 50 35 26 34 23 58 16
AAG 10 11 63 13 16 13 18 22 32
ATG 8 10 16 9 10 20 14 24 12
TTT 21 11 19 15 9 17 15 28 19
TTC 9 5 24 14 5 16 16 18 11
CCT 9 9 17 9 6 5 7 20 11
CCC 3 0 2 3 1 4 4 9 6
CCA 11 6 31 11 10 10 8 14 3
CCG 2 2 2 5 2 3 4 11 7
TCT 9 7 27 9 4 10 13 14 6
TCC 9 4 16 16 1 10 4 6 9
TCA 14 3 6 8 10 13 3 13 9
TCG 5 8 5 4 4 9 6 4 6
AGT 4 8 6 7 6 4 1 12 9
AGC 3 3 7 4 6 5 1 10 5
TAA 0 0 0 0 1 1 1 1 1
TAG 0 0 1 0 0 0 0 0 0
TGA 1 1 0 1 0 0 0 0 0
ACT 15 5 35 6 4 5 11 18 9
ACC 9 1 17 4 7 6 0 11 5
ACA 8 7 8 8 6 8 4 11 5
ACG 3 4 2 5 5 6 5 6 10
TGG 8 4 25 11 4 8 10 19 4
TAT 13 8 16 16 6 15 7 16 9
TAC 7 4 19 9 9 9 8 11 11
GTT 12 12 45 15 8 14 7 18 9
GTC 3 4 17 3 2 6 2 14 9
GTA 3 9 6 8 9 11 6 15 7
GTG 4 4 1 6 3 9 5 14 4
YOL033W YPL040C YPL097W YPL104W YPR033C YPR047W YNL247W YPR081C YBL076C
GCT 8 12 12 12 29 5 23 6 26
GCC 5 8 3 11 10 4 14 4 18
GCA 9 17 3 9 10 1 11 9 11
GCG 5 5 5 3 3 3 1 2 1
CGT 2 4 3 3 4 4 3 3 15
CGC 1 7 0 1 0 3 3 2 1
CGA 3 4 5 2 1 1 0 5 0
CGG 3 0 2 2 0 0 0 1 1
AGA 14 18 7 17 11 16 16 16 28
AGG 6 13 11 9 6 4 2 9 1
AAT 12 29 19 26 11 16 27 22 19
AAC 14 22 10 11 5 11 23 12 27
GAT 22 36 20 25 24 23 34 23 48
GAC 6 16 9 14 11 9 19 13 30
TGT 10 11 6 3 5 1 4 6 9
TGC 1 3 1 5 0 5 2 2 0
CAA 9 32 11 13 12 9 28 13 20
CAG 6 17 11 10 4 3 9 12 4
GAA 22 53 15 28 31 24 38 32 59
GAG 13 14 5 18 9 11 15 14 20
GGT 11 12 12 14 30 2 17 15 43
GGC 4 12 5 7 7 6 11 4 7
GGA 7 18 13 7 2 8 5 10 6
GGG 6 5 4 4 1 3 1 8 1
CAT 9 25 5 10 2 9 15 9 13
CAC 7 9 3 2 4 5 1 4 7
ATT 9 29 13 18 20 16 29 22 44
ATC 8 20 11 13 15 8 19 10 20
ATA 18 23 11 12 4 11 3 12 3
TTA 15 34 16 16 14 9 25 16 34
TTG 22 26 16 20 18 12 28 23 46
CTT 10 16 6 4 4 8 3 4 7
CTC 1 10 4 6 1 4 0 2 1
CTA 10 23 8 8 6 6 8 7 7
CTG 7 10 5 8 1 4 2 6 4
AAA 28 50 23 37 25 26 40 29 50
AAG 23 29 11 24 29 14 37 17 43
ATG 12 15 7 15 12 14 12 18 18
TTT 21 25 15 31 10 13 23 24 22
TTC 5 13 7 8 10 6 15 15 31
CCT 12 11 6 8 7 6 9 8 14
CCC 3 9 5 4 1 4 5 4 2
CCA 9 13 5 18 7 7 13 8 28
CCG 2 8 0 4 0 3 3 5 1
TCT 17 14 8 11 21 9 14 5 26
TCC 3 15 6 6 8 4 16 7 21
TCA 6 20 11 9 9 14 9 10 12
TCG 6 6 4 4 2 0 4 11 1
AGT 3 11 11 12 5 3 6 6 8
AGC 4 13 3 3 1 3 5 1 3
TAA 1 0 1 0 1 0 0 1 0
TAG 0 0 0 0 0 1 1 0 0
TGA 0 1 0 1 0 0 0 0 1
ACT 5 17 9 7 14 9 19 16 25
ACC 7 11 1 8 5 7 11 5 17
ACA 5 16 9 10 7 9 8 10 12
ACG 7 8 6 5 2 4 5 7 4
TGG 5 18 3 5 4 10 14 6 22
TAT 15 25 12 13 10 10 9 5 25
TAC 5 17 7 9 7 5 12 8 22
GTT 6 19 9 12 19 10 19 10 44
GTC 6 9 4 5 10 4 9 6 24
GTA 4 8 10 8 2 11 3 9 5
GTG 2 9 10 11 4 5 8 10 11
YBR121C YDR023W YDR037W YDR341C YER087W YFL022C YGL245W YGR185C YGR264C
GCT 25 16 21 18 10 10 35 11 22
GCC 17 6 14 10 3 12 13 9 11
GCA 7 1 1 11 6 4 3 6 13
GCG 0 1 1 4 5 1 1 5 1
CGT 5 4 9 7 4 4 10 0 10
CGC 2 0 1 1 2 0 0 0 1
CGA 0 0 0 0 3 0 0 0 0
CGG 0 0 0 0 1 0 0 0 0
AGA 26 12 23 19 12 15 23 8 12
AGG 3 1 2 1 6 0 3 2 1
AAT 13 11 10 13 24 9 15 9 30
AAC 10 12 11 13 11 17 21 12 24
GAT 29 17 24 22 31 15 43 10 30
GAC 20 7 17 12 10 20 21 8 15
TGT 6 5 8 2 11 1 6 3 10
TGC 0 3 1 1 4 0 1 1 0
CAA 15 17 24 20 11 20 16 15 24
CAG 1 4 2 4 11 5 0 2 3
GAA 52 40 46 36 27 26 44 23 44
GAG 9 11 9 14 10 12 2 7 7
GGT 30 21 29 28 14 21 24 17 29
GGC 5 2 2 7 8 2 6 4 2
GGA 4 3 1 3 11 1 6 1 5
GGG 2 0 1 0 3 4 1 1 1
CAT 12 5 7 7 8 4 4 3 17
CAC 3 4 9 7 5 8 10 2 5
ATT 21 12 17 22 13 9 28 9 23
ATC 14 13 10 18 11 17 18 12 15
ATA 2 1 1 1 14 1 4 0 3
TTA 18 17 12 24 17 7 19 10 22
TTG 32 17 27 18 15 23 32 19 34
CTT 3 2 5 6 5 9 1 4 4
CTC 0 1 1 1 2 4 1 2 1
CTA 2 4 5 6 6 7 7 5 8
CTG 1 0 2 6 11 8 1 1 6
AAA 30 24 23 29 35 20 27 21 34
AAG 30 26 25 22 15 21 49 21 28
ATG 12 6 20 19 16 14 17 9 10
TTT 22 7 13 15 18 7 8 12 18
TTC 11 13 17 14 5 19 21 8 14
CCT 7 3 7 5 6 8 8 6 9
CCC 0 1 0 3 4 4 2 2 1
CCA 23 15 23 11 9 8 20 17 24
CCG 0 0 3 1 1 0 0 1 0
TCT 19 12 11 15 5 11 13 5 22
TCC 11 10 7 5 4 12 6 5 7
TCA 4 3 3 5 14 3 5 3 10
TCG 0 0 1 3 6 4 1 1 5
AGT 5 3 0 1 11 0 2 3 7
AGC 0 1 1 2 5 1 3 2 3
TAA 1 1 1 1 0 1 1 1 1
TAG 0 0 0 0 1 0 0 0 0
TGA 0 0 0 0 0 0 0 0 0
ACT 13 7 12 11 8 5 20 5 11
ACC 9 4 10 5 4 16 13 8 2
ACA 4 1 7 8 8 6 2 2 12
ACG 2 1 0 1 2 3 2 2 7
TGG 7 6 2 9 10 6 12 1 13
TAT 10 8 7 13 8 3 8 7 20
TAC 8 13 13 11 10 12 15 6 15
GTT 33 15 15 24 10 9 22 14 32
GTC 17 8 14 8 7 12 22 8 7
GTA 1 4 3 3 6 0 1 1 1
GTG 0 1 1 2 4 3 6 3 6
YHR019C YIL078W YLR060W YOL097C YOR335C YPL160W YHR020W YOR168W YLL018C
GCT 20 17 16 6 39 43 25 20 21
GCC 12 17 16 7 19 24 17 7 14
GCA 9 3 3 7 8 24 7 15 8
GCG 0 2 2 2 2 6 0 6 0
CGT 9 10 7 4 12 15 5 3 10
CGC 1 0 0 1 1 1 2 0 1
CGA 0 0 0 0 0 0 0 0 0
CGG 0 0 0 0 0 0 0 0 0
AGA 17 27 17 10 20 20 26 14 19
AGG 0 2 1 1 2 5 3 5 6
AAT 4 12 14 7 27 18 13 15 4
AAC 8 20 18 4 23 21 10 12 12
GAT 11 30 22 20 49 50 29 16 10
GAC 26 14 18 15 24 14 20 9 23
TGT 8 9 8 5 6 11 6 7 3
TGC 1 3 1 1 1 2 0 2 0
CAA 20 23 15 19 23 31 15 14 18
CAG 4 4 3 3 3 6 1 1 5
GAA 34 56 31 22 66 81 52 29 43
GAG 10 8 16 6 12 18 9 8 14
GGT 27 31 18 17 60 42 30 17 27
GGC 6 5 6 4 10 9 5 3 1
GGA 3 6 0 2 3 3 4 13 0
GGG 1 5 4 2 3 6 2 3 4
CAT 8 13 7 7 11 12 12 9 4
CAC 2 6 8 2 5 8 3 5 8
ATT 13 21 20 11 29 46 21 24 16
ATC 14 13 19 6 24 22 14 11 12
ATA 1 1 4 2 3 6 2 9 0
TTA 7 21 15 7 20 28 18 13 6
TTG 35 31 25 16 38 30 32 21 36
CTT 1 1 5 3 8 5 3 8 3
CTC 2 0 0 0 1 1 0 1 2
CTA 5 6 8 4 6 9 2 9 7
CTG 4 3 2 3 6 4 1 4 2
AAA 13 32 23 18 39 47 30 24 16
AAG 30 33 23 26 52 53 30 15 32
ATG 11 22 13 8 10 27 12 16 11
TTT 7 18 13 16 26 30 22 10 12
TTC 15 21 16 19 27 29 11 5 16
CCT 3 4 7 7 11 19 7 11 7
CCC 2 0 0 1 4 1 0 3 5
CCA 17 22 21 12 22 29 23 15 14
CCG 0 2 2 1 1 3 0 3 0
TCT 13 28 11 3 25 28 19 16 7
TCC 13 7 13 9 11 6 11 9 10
TCA 3 3 5 4 8 12 4 6 2
TCG 1 2 4 2 1 2 0 1 1
AGT 2 6 2 1 3 3 5 5 5
AGC 3 1 3 5 2 5 0 2 3
TAA 0 1 1 1 1 1 1 1 0
TAG 0 0 0 0 0 0 0 0 0
TGA 1 0 0 0 0 0 0 0 1
ACT 12 18 9 9 26 23 13 9 5
ACC 17 10 14 10 13 15 9 4 13
ACA 5 2 4 6 8 13 4 12 6
ACG 2 0 3 2 1 6 2 6 1
TGG 4 13 4 3 8 13 7 1 1
TAT 10 8 4 3 13 26 10 9 6
TAC 13 16 13 9 22 26 8 7 12
GTT 13 24 17 12 36 25 33 18 11
GTC 15 18 12 8 16 17 17 11 11
GTA 4 3 6 5 3 8 1 10 4
GTG 3 1 4 7 6 3 0 10 7
Duality diagramm
class: coa dudi
$call: dudi.coa(df = aminoacyl$usage.codon, scannf = FALSE)
$nf: 2 axis-components saved
$rank: 34
eigen values: 0.07774 0.01301 0.008387 0.007261 0.006383 ...
vector length mode content
1 $cw 36 numeric column weights
2 $lw 64 numeric row weights
3 $eig 34 numeric eigen values
data.frame nrow ncol content
1 $tab 64 36 modified array
2 $li 64 2 row coordinates
3 $l1 64 2 row normed scores
4 $co 36 2 column coordinates
5 $c1 36 2 column normed scores
other elements: N
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