ライフサイエンスコーパス: codon usage bias

1 otential bias in the methods used to measure codon usage bias.

2 ution between species than do genes with low codon usage bias.

3 d constraint appears to be a major driver of codon usage bias.

4 was put forward to explain the existence of codon usage bias.

5 , more tRNA genes and more strongly selected codon usage bias.

6 errors can play an important role in shaping codon usage bias.

7 to use G/C-ending codons together with more codon usage bias.

8 fast-evolving nonsynonymous sites have lower codon usage bias.

9 re used to analyze both base composition and codon usage bias.

10 on of Li's protocol but that also allows for codon usage bias.

11 te the transition/transversion rate bias and codon usage bias.

12 osophila melanogaster have relatively higher codon usage biases.

13 Differences in codon usage bias across genes reveal that weak selection

14 as expression-related or GC-content-related codon usage bias, also affect volatility.

15 ebserver service as a user-friendly tool for codon usage bias analyses across and within genomes in r

16 A codon usage bias pipeline is demanding for codon usage bias analyses within and across genomes.

17 Strong relationships between synonymous codon usage bias and estimates of transcript abundance s

18 other bacteria and, along with their similar codon usage bias and G + C content, suggests acquisition

19 The different relationships between codon usage bias and gene length observed in prokaryotes

20 tes, these footprints are seen in the higher codon usage bias and lower synonymous divergence.

21 Finally, analyses of codon usage bias and RNA-editing processes of the conoto

22 ion of both selection and mutational bias on codon usage bias and suggest that codon usage and genome

23 s synthesized incorporating Escherichia coli codon usage bias and was used to express biologically ac

24 ation pattern or in tDNA copy number changed codon-usage bias and increased the K(S) distance between

25 orthologues in non-WGD species, we show that codon-usage bias and protein-sequence conservation are t

26 n bias is likely toward A+T (the opposite of codon usage bias), and not all amino acids display the p

27 oth yeast and fruit fly, spatial patterns of codon usage bias are characteristically different from p

28 tution rates and between synonymous rate and codon usage bias are important to our understanding of t

29 y to common belief, amino acid (AA) bias and codon usage bias are insufficient to create base-3 perio

30 This revealed that patterns of codon usage bias are strongly correlated with overall ge

31 Synonymous codon usage biases are associated with various biologica

32 Differences between codon usage biases are attributed, in part, to changes i

33 Codon usage biases are found in all eukaryotic and proka

34 We employ synonymous codon usage bias as a measure of translation rates and s

35 Using synonymous codon usage bias as a measure of translation rates, we s

36 highly expressed proteins (with adherence to codon usage bias as a proxy for expressivity) to utilize

37 recombination, saturation, and variation in codon usage bias as factors contributing to this high le

38 sts itself even in the absence of synonymous codon usage bias at the 4-fold degenerate sites.

39 are an interesting system in which to study codon usage bias because of their length, expression, an

40 that the combination of nonsense errors and codon usage bias can have a large effect on the probabil

41 howing that fast-evolving genes have a lower codon usage bias, consistent with strong positive select

42 as used to test whether base composition and codon usage bias covary with arthropod association in th

43 Most previous studies of the evolution of codon usage bias (CUB) and intronic GC content (iGC) in

44 nonadaptive forces driving the evolution of codon usage bias (CUB) has been an area of intense focus

45 Codon usage bias (CUB) has been documented across a wide

46 regarded as a model organism in the study of codon usage bias (CUB).

47 Surprisingly, we find that genes with higher codon usage bias display higher levels of intraspecific

48 The synonymous codon usage bias (EN(C)) values suggest greater variabil

49 d nonsynonymous nucleotide substitutions and codon usage bias (ENC) were estimated for a number of nu

50 ce of organisms with varying GC composition, codon usage biases etc., and consequently gene identific

51 e of non-synonymous substitutions (d(N)) and codon usage bias (F(op)), showing that fast-evolving gen

52 nylation signal in the 3' UTR, a distinctive codon usage bias for A or T in the third position and an

53 ute the position-specific scoring matrix and codon usage bias for all such RNA sequences.

54 Accurately quantifying codon usage bias for different organisms is useful not o

55 Codon-usage bias has been observed in almost all genomes

56 uggesting that genes with a higher degree of codon usage bias have evolved at a slower rate.

57 A evolution and confirm that genes with high codon usage bias have lower rates of synonymous substitu

58 Quantification of codon usage bias helps understand evolution of living or

59 ncreases in S288c occur in genes with strong codon usage bias; (iii) genes under stronger negative se

60 Reduced codon usage bias in D. miranda may thus result from the

61 first review what is known about patterns of codon usage bias in Drosophila and make the following po

62 Codon usage bias in Drosophila melanogaster genes has be

63 thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutationa

64 ntragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli,

65 hts into protein maturation and homeostasis, codon usage bias in organisms, the origins of translatio

66 play a strong role in inflating the level of codon usage bias in rbcL, despite the fact that twofolds

67 Further, we find highly significant codon usage bias in regions downstream of the PTC in 38

68 n this study we reconstruct the evolution of codon usage bias in the chloroplast gene rbcL using a ph

69 Here, we show that there is a strong codon usage bias in the filamentous fungus Neurospora.

70 Because a strong synonymous codon usage bias in the human DRD2 gene, suggesting sele

71 The low codon usage bias in the middle region is best explained

72 show that in yeast and prokaryotic genomes, codon usage bias increases along translational direction

73 is negatively correlated with the degree of codon usage bias, indicating stronger selection on codon

74 we calibrated each genome in turn using the codon usage bias indices of highly expressed ribosomal p

75 We here introduce an explicit model of codon usage bias, inspired by statistical physics.

76 Synonymous codon usage bias is a broadly observed phenomenon in bac

77 Codon usage bias is a ubiquitous phenomenon, which may b

78 Codon usage bias is a universal feature of all genomes,

79 Codon usage bias is a universal feature of eukaryotic an

80 The pattern of its codon usage bias is also consistent with that of HAV.

81 It was demonstrated that codon usage bias is correlated positively with gene tran

82 Synonymous codon usage bias is determined by a combination of mutat

83 ffect of expression level on the strength of codon usage bias is more conspicuous than its effect on

84 Codon usage bias is the nonrandom use of synonymous codo

85 This suggests that codon usage bias may be constrained by particular amino

86 centralized repository of look-up tables and codon usage bias measures for a wide variety of genera,

87 Codon usage bias of 1,117 Drosophila melanogaster genes,

88 ibute significantly and about equally to the codon usage bias of a gene.

89 ino acids that contributed most to the total codon usage bias of each taxon are known through amino a

90 virus attenuation strategy makes use of the codon usage biases of human and avian influenza viruses

91 e usually encoded by optimal codons, yet the codon-usage bias of the kaiBC genes is not optimized for

92 Given the impact of codon usage bias on recombinant gene technologies, this

93 is effective only in the presence of strong codon-usage bias or protein-sequence conservation.

94 A codon usage bias pipeline is demanding for codon usage b

95 A variety of factors, including gene length, codon usage bias, protein abundance, protein function, a

96 The strength of selected codon usage bias, S, is found to vary substantially amon

97 ow a negative association with the degree of codon usage bias, suggesting that genes with a higher de

98 ymous to synonymous substitutions, and lower codon usage bias than other genes, suggesting that Cs is

99 We employ a measure of codon usage bias that accounts for chloroplast genomic n

100 Codon usage bias, the preferential use of particular cod

101 nergetically costly longer genes have higher codon usage bias to maximize translational efficiency.

102 The gene shows a codon usage bias typical of non-nif and non-fix genes fr

103 e pattern of non-uniform codon use (known as codon usage bias) varies between organisms and represent

104 e conclusion that the formation of G. biloba codon usage bias was dominated by natural selection.

105 ationship between gene length and synonymous codon usage bias was investigated in Drosophila melanoga

106 Furthermore, codon usage bias was relaxed for these genes in post-WGD

107 redicted expression level of a gene based on codon usage biases was ascertained, such that predicted

108 efficiency, and the Hill-Robertson effect in codon usage bias, we studied the intragenic spatial dist

109 Many genes exhibit little codon-usage bias, which is thought to reflect a lack of

110 nearly symmetric M-shaped spatial pattern of codon usage bias, with less bias in the middle and both

111 equally and highly significantly to overall codon usage bias, with the exception of Asp which had ve

112 mutational biases contribute to variation in codon usage bias within Drosophila species.