Mesoplasma florum:Codon usage: Difference between revisions

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The codon usage table for Mesoplasma florum is here:
The Mesoplasma florum codon usage table is here.  Also in this table are the probabilities for E. coli codons, and a compromise codon probability calculated by taking the geometric mean of the two genome codon probabilities and renormalizing such that the sum of probabilities of each codon for a specific amino acid is unity.
 
A computer readable version of this compromise codon table is here, suitable for use with the DNA2.0 Gene Designer software available [http://www.dna20.com/index.php?pageID=216 here].  [[media:mf-ec-codon.txt | Compromise codon table]]
Mesoplasma florum L1 [gbbct]: 683 CDS's (245761 codons)
AmAcid  Codon      Number    /1000    Fraction  ..
   


{| border="1"
{| border="1"
Line 20: Line 17:
|3.45
|3.45
|0.06
|0.06
|
|.15
|
|.12
|-
|-
|Gly
|Gly
Line 28: Line 25:
|23.26
|23.26
|0.43
|0.43
|
|.11
|
|.26
|-
|-
|Gly
|Gly
Line 36: Line 33:
|25.01
|25.01
|0.47
|0.47
|
|.34
|
|.49
|-
|-
|Gly
|Gly
Line 44: Line 41:
|1.88
|1.88
|0.03
|0.03
|
|.40
|
|.13
|-
|-
|Glu
|Glu
Line 52: Line 49:
|6.28
|6.28
|0.09
|0.09
|
|.31
|
|.17
|-
|-
|Glu
|Glu
Line 60: Line 57:
|66.34
|66.34
|0.91
|0.91
|
|.69
|
|.83
|-
|-
|Asp
|Asp
Line 68: Line 65:
|44.43
|44.43
|0.83
|0.83
|
|.63
|
|.74
|-
|-
|Asp
|Asp
Line 76: Line 73:
|8.96
|8.96
|0.17
|0.17
|
|.37
|
|.26
|-
|-
|Val
|Val
Line 84: Line 81:
|2.57
|2.57
|0.04
|0.04
|
|.37
|
|.15
|-
|-
|Val
|Val
Line 92: Line 89:
|17.24
|17.24
|0.28
|0.28
|
|.15
|
|.25
|-
|-
|Val
|Val
Line 100: Line 97:
|39.31
|39.31
|0.65
|0.65
|
|.26
|
|.52
|-
|-
|Val
|Val
Line 108: Line 105:
|1.40
|1.40
|0.02
|0.02
|
|.22
|
|.08
|-
|-
|Ala
|Ala
Line 116: Line 113:
|2.11
|2.11
|0.04
|0.04
|
|.36
|
|.15
|-
|-
|Ala
|Ala
Line 124: Line 121:
|25.22
|25.22
|0.46
|0.46
|
|.21
|
|.38
|-
|-
|Ala
|Ala
Line 132: Line 129:
|25.62
|25.62
|0.47
|0.47
|
|.16
|
|.34
|-
|-
|Ala
|Ala
Line 140: Line 137:
|2.12
|2.12
|0.04
|0.04
|
|.27
|
|.13
|-
|Arg
|AGG
|194
|0.79
|0.03
|.02
|.05
|-
|Arg
|AGA
|5448
|22.17
|0.80
|.04
|.33
|-
|Ser
|AGT
|3752
|15.27
|0.23
|.15
|.23
|-
|Ser
|AGC
|935
|3.80
|0.06
|.28
|.16
|-
|Lys
|AAG
|2110
|8.59
|0.09
|.23
|.15
|-
|Lys
|AAA
|21721
|88.38
|0.91
|.77
|.85
|-
|Asn
|AAT
|13612
|55.39
|0.77
|.45
|.62
|-
|Asn
|AAC
|4161
|16.93
|0.23
|.55
|.38
|-
|Met
|ATG
|5660
|23.03
|1.00
|1.00
|1.00
|-
|Ile
|ATA
|7748
|31.53
|0.32
|.07
|.17
|-
|Ile
|ATT
|14701
|59.82
|0.60
|.51
|.62
|-
|Ile
|ATC
|1968
|8.01
|0.08
|.42
|.21
|-
|Thr
|ACG
|211
|0.86
|0.02
|.27
|.10
|-
|Thr
|ACA
|7243
|29.47
|0.55
|.13
|.38
|-
|Thr
|ACT
|5558
|22.62
|0.42
|.17
|.38
|-
|Thr
|ACC
|274
|1.11
|0.02
|.44
|.14
|-
|Trp
|TGG
|101
|0.41
|0.04
|1.00
|1.00
|-
|Trp
|TGA
|2489
|10.13
|0.96
|0.0
|0.0
|-
|Cys
|TGT
|1275
|5.19
|0.85
|.45
|.68
|-
|Cys
|TGC
|228
|0.93
|0.15
|.55
|.32
|-
|End
|TAG
|132
|0.54
|0.19
|.07
|.14
|-
|End
|TAA
|551
|2.24
|0.81
|.64
|.86
|-
|Tyr
|TAT
|7191
|29.26
|0.78
|.57
|.68
|-
|Tyr
|TAC
|1972
|8.02
|0.22
|.43
|.32
|-
|-
!}
|Leu
|TTG
|1765
|7.18
|0.08
|.13
|.16
|-
|Leu
|TTA
|15736
|64.03
|0.71
|.13
|.49
|-
|Phe
|TTT
|10293
|41.88
|0.81
|.57
|.70
|-
|Phe
|TTC
|2391
|9.73
|0.19
|.43
|.30
|-
|Ser
|TCG
|206
|0.84
|0.01
|.16
|.05
|-
|Ser
|TCA
|7413
|30.16
|0.46
|.12
|.29
|-
|Ser
|TCT
|3585
|14.59
|0.22
|.15
|.22
|-
|Ser
|TCC
|92
|0.37
|0.01
|.15
|.05
|-
|Arg
|CGG
|6
|0.02
|0.00
|.10
|0.0
|-
|Arg
|CGA
|128
|0.52
|0.02
|.06
|.06
|-
|Arg
|CGT
|998
|4.06
|0.15
|.38
|.44
|-
|Arg
|CGC
|67
|0.27
|0.01
|.40
|.12
|-
|Gln
|CAG
|404
|1.64
|0.05
|.65
|.24
|-
|Gln
|CAA
|7058
|28.72
|0.95
|.35
|.76
|-
|His
|CAT
|2211
|9.00
|0.73
|.57
|.65
|-
|His
|CAC
|836
|3.40
|0.27
|.43
|.35
|-
|Leu
|CTG
|182
|0.74
|0.01
|.50
|.11
|-
|Leu
|CTA
|1690
|6.88
|0.08
|.04
|.08
|-
|Leu
|CTT
|2682
|10.91
|0.12
|.10
|.17
|-
|Leu
|CTC
|52
|0.21
|0.00
|.10
|0.0
|-
|Pro
|CCG
|203
|0.83
|0.03
|.52
|.16
|-
|Pro
|CCA
|3516
|14.31
|0.57
|.19
|.44
|-
|Pro
|CCT
|2306
|9.38
|0.37
|.16
|.32
|-
|Pro
|CCC
|157
|0.64
|0.03
|.12
|.08
|-
|}


|Arg    AGG      194.00      0.79      0.03
[[Category:Mesoplasma florum]]
|Arg    AGA      5448.00    22.17      0.80
|Ser    AGT      3752.00    15.27      0.23
|Ser    AGC      935.00      3.80      0.06
Lys    AAG      2110.00      8.59      0.09
Lys    AAA    21721.00    88.38      0.91
Asn    AAT    13612.00    55.39      0.77
Asn    AAC      4161.00    16.93      0.23
Met    ATG      5660.00    23.03      1.00
Ile    ATA      7748.00    31.53      0.32
Ile    ATT    14701.00    59.82      0.60
Ile    ATC      1968.00      8.01      0.08
Thr    ACG      211.00      0.86      0.02
Thr    ACA      7243.00    29.47      0.55
Thr    ACT      5558.00    22.62      0.42
Thr    ACC      274.00      1.11      0.02
Trp    TGG      101.00      0.41      0.04
Trp    TGA      2489.00    10.13      0.96
Cys    TGT      1275.00      5.19      0.85
Cys    TGC      228.00      0.93      0.15
End    TAG      132.00      0.54      0.19
End    TAA      551.00      2.24      0.81
Tyr    TAT      7191.00    29.26      0.78
Tyr    TAC      1972.00      8.02      0.22
Leu    TTG      1765.00      7.18      0.08
Leu    TTA    15736.00    64.03      0.71
Phe    TTT    10293.00    41.88      0.81
Phe    TTC      2391.00      9.73      0.19
Ser    TCG      206.00      0.84      0.01
Ser    TCA      7413.00    30.16      0.46
Ser    TCT      3585.00    14.59      0.22
Ser    TCC        92.00      0.37      0.01
Arg    CGG        6.00      0.02      0.00
Arg    CGA      128.00      0.52      0.02
Arg    CGT      998.00      4.06      0.15
Arg    CGC        67.00      0.27      0.01
Gln    CAG      404.00      1.64      0.05
Gln    CAA      7058.00    28.72      0.95
His    CAT      2211.00      9.00      0.73
His    CAC      836.00      3.40      0.27
Leu    CTG      182.00      0.74      0.01
Leu    CTA      1690.00      6.88      0.08
Leu    CTT      2682.00    10.91      0.12
Leu    CTC        52.00      0.21      0.00
Pro    CCG      203.00      0.83      0.03
Pro    CCA      3516.00    14.31      0.57
Pro    CCT      2306.00      9.38      0.37
Pro    CCC      157.00      0.64      0.03
 
 
|}

Latest revision as of 08:45, 17 September 2009

The Mesoplasma florum codon usage table is here. Also in this table are the probabilities for E. coli codons, and a compromise codon probability calculated by taking the geometric mean of the two genome codon probabilities and renormalizing such that the sum of probabilities of each codon for a specific amino acid is unity. A computer readable version of this compromise codon table is here, suitable for use with the DNA2.0 Gene Designer software available here. Compromise codon table

Amino acid Codon Number Number / 1000 Probability EC Probability Compromise Probability
Gly GGG 848 3.45 0.06 .15 .12
Gly GGA 5717 23.26 0.43 .11 .26
Gly GGT 6147 25.01 0.47 .34 .49
Gly GGC 461 1.88 0.03 .40 .13
Glu GAG 1543 6.28 0.09 .31 .17
Glu GAA 16303 66.34 0.91 .69 .83
Asp GAT 10918 44.43 0.83 .63 .74
Asp GAC 2203 8.96 0.17 .37 .26
Val GTG 632 2.57 0.04 .37 .15
Val GTA 4237 17.24 0.28 .15 .25
Val GTT 9660 39.31 0.65 .26 .52
Val GTC 344 1.40 0.02 .22 .08
Ala GCG 519 2.11 0.04 .36 .15
Ala GCA 6198 25.22 0.46 .21 .38
Ala GCT 6297 25.62 0.47 .16 .34
Ala GCC 522 2.12 0.04 .27 .13
Arg AGG 194 0.79 0.03 .02 .05
Arg AGA 5448 22.17 0.80 .04 .33
Ser AGT 3752 15.27 0.23 .15 .23
Ser AGC 935 3.80 0.06 .28 .16
Lys AAG 2110 8.59 0.09 .23 .15
Lys AAA 21721 88.38 0.91 .77 .85
Asn AAT 13612 55.39 0.77 .45 .62
Asn AAC 4161 16.93 0.23 .55 .38
Met ATG 5660 23.03 1.00 1.00 1.00
Ile ATA 7748 31.53 0.32 .07 .17
Ile ATT 14701 59.82 0.60 .51 .62
Ile ATC 1968 8.01 0.08 .42 .21
Thr ACG 211 0.86 0.02 .27 .10
Thr ACA 7243 29.47 0.55 .13 .38
Thr ACT 5558 22.62 0.42 .17 .38
Thr ACC 274 1.11 0.02 .44 .14
Trp TGG 101 0.41 0.04 1.00 1.00
Trp TGA 2489 10.13 0.96 0.0 0.0
Cys TGT 1275 5.19 0.85 .45 .68
Cys TGC 228 0.93 0.15 .55 .32
End TAG 132 0.54 0.19 .07 .14
End TAA 551 2.24 0.81 .64 .86
Tyr TAT 7191 29.26 0.78 .57 .68
Tyr TAC 1972 8.02 0.22 .43 .32
Leu TTG 1765 7.18 0.08 .13 .16
Leu TTA 15736 64.03 0.71 .13 .49
Phe TTT 10293 41.88 0.81 .57 .70
Phe TTC 2391 9.73 0.19 .43 .30
Ser TCG 206 0.84 0.01 .16 .05
Ser TCA 7413 30.16 0.46 .12 .29
Ser TCT 3585 14.59 0.22 .15 .22
Ser TCC 92 0.37 0.01 .15 .05
Arg CGG 6 0.02 0.00 .10 0.0
Arg CGA 128 0.52 0.02 .06 .06
Arg CGT 998 4.06 0.15 .38 .44
Arg CGC 67 0.27 0.01 .40 .12
Gln CAG 404 1.64 0.05 .65 .24
Gln CAA 7058 28.72 0.95 .35 .76
His CAT 2211 9.00 0.73 .57 .65
His CAC 836 3.40 0.27 .43 .35
Leu CTG 182 0.74 0.01 .50 .11
Leu CTA 1690 6.88 0.08 .04 .08
Leu CTT 2682 10.91 0.12 .10 .17
Leu CTC 52 0.21 0.00 .10 0.0
Pro CCG 203 0.83 0.03 .52 .16
Pro CCA 3516 14.31 0.57 .19 .44
Pro CCT 2306 9.38 0.37 .16 .32
Pro CCC 157 0.64 0.03 .12 .08
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