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

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

4 elanogaster for distinct tissue responses to codon usage bias.

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

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

7 in different organisms, a phenomenon termed codon usage bias.

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

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

10 ated to but clearly distinct from individual codon usage bias.

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

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

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

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

15 osophila melanogaster have relatively higher codon usage biases.

16 Codon usage bias, a universal feature of all genomes, pl

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

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

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

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

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

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

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

24 Genomic traits such as codon usage bias and genome size have been linked to bac

25 translational efficiency and accuracy drive codon usage bias and its coevolution with the tRNA pool.

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

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

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

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

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

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

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

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

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

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

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

37 Synonymous codon usage biases are associated with various biologica

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

39 Codon usage biases are found in all eukaryotic and proka

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

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

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

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

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

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

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

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

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

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

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

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

52 This codon usage bias (CUB) is highly variable across species

53 Codon usage bias (CUB), where certain codons are used mo

54 ed with equal frequency, a phenomenon termed codon usage bias (CUB).

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

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

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

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

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

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

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

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

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

64 Codon usage bias has long been appreciated to influence

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

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

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

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

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

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

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

72 Codon usage bias in Drosophila melanogaster genes has be

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

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

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

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

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

78 tRNA genes, total number of rRNA genes, and codon usage bias in ribosomal protein sequences were all

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

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

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

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

83 e water limited and pulse driven-have higher codon usage bias in their ribosomal protein genes.

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

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

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

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

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

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

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

91 Codon usage bias is a universal feature of all genomes.

92 Codon usage bias is a universal feature of eukaryotic an

93 Codon usage bias is a universal feature of eukaryotic an

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

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

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

97 g translational accuracy hypothesis (TAH) of codon usage bias is higher translational accuracies of m

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

99 host cell for protein translation, but their codon usage bias is often different from that of the hos

100 Codon usage bias is the nonrandom use of synonymous codo

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

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

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

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

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

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

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

108 optimization tool, ICOR, that aims to learn codon usage bias on a genomic dataset of Escherichia col

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

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

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

112 Codon usage biases play a significant role in determinin

113 These results indicate that codon usage bias plays a more nuanced role in controllin

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

115 , sampling to maximize sequence diversity or codon usage bias reduces performance substantially.

116 However, population-specific differences in codon usage biases remain largely unexplored.

117 In addition, codon usage biases result in nonuniform ribosome decodin

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

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

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

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

122 Codon usage bias, the preference for certain synonymous

123 Codon usage bias, the preferential use of particular cod

124 Codon usage bias-the preferential use of certain synonym

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

126 p codons in ciliates may have coevolved with codon usage biases to avoid triplet repeat disorders med

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

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

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

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

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

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

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

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

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

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

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