ライフサイエンスコーパス: base composition

1 at account for nearest-neighbor frequency or base composition.

2 g sites, while accounting for differences in base composition.

3 221,459 bp in length and possesses a 49% G+C base composition.

4 tabilize parallel DNA triplexes of different base composition.

5 mentary strands of DNA tend to have the same base composition.

6 d from the 3' end of a template depending on base composition.

7 olymerase kinetics are related to nucleotide base composition.

8 e on different chromosomes and vary in their base composition.

9 aryotes, has a wide heterogeneity in the DNA base composition.

10 scripts were characterized in terms of their base composition.

11 or non-coding native DNA with such anomalous base composition.

12 fferent length third-strand loops of various base composition.

13 age T7, we analyzed its genome for a bias in base composition.

14 no such alternation despite having the same base composition.

15 might be influencing genome-wide patterns of base composition.

16 ar species' genome are relatively similar in base composition.

17 y from O4'-endo to C2'-endo depending on the base composition.

18 s or MARs) than would be expected from their base composition.

19 etween strands using measures independent of base composition.

20 convenient binding platforms of programmable base composition.

21 l genes could help shape the overall genomic base composition.

22 demonstrates the impact of recombination on base composition.

23 ce for the substantial bias depending on the base composition.

24 ns with relatively homogeneous within-region base composition.

25 ontain modifications affecting expression or base composition.

26 l accumulation is practically independent of base composition.

27 ry factor was correlated strongly with local base composition.

28 ogeneous due to short segments with distinct base compositions.

29 ude for ssDNAs of different nearest-neighbor base compositions.

30 ions of the sequences, rather than to simple base compositions.

31 convergence of SAR11 and Rickettsiales tRNA base compositions.

32 ariability in tRNA gene complement sizes and base compositions.

33 th sharp peaks defined by highly constrained base compositions.

34 timating divergence should take into account base composition; (3) only very closely related species

35 on of genetic properties including AT-biased base composition, accelerated sequence evolution, and, a

36 cating that there is systematic variation in base composition across their genomes.

37 With base-composition across polymorphic sites as a genome ph

38 Codon usage and base composition also followed canonical vertebrate patt

39 odon choice, while still preserving original base composition, also results in less stable mRNAs.

40 In terms of base composition, although the intergenic regions of the

41 Likewise, stationarity of base composition among Buchnera species indicated equal

42 onization mass spectrometry (PCR/ESI-MS) and base composition analysis of PCR amplification products

43 lectrospray ionization mass spectrometry and base composition analysis of PCR amplification products

44 ange and reverse phase) and characterised by base composition analysis.

45 ay ionization mass spectrometry and amplicon base composition analysis.

46 Conservation in 3'UTRs correlates with their base composition and also with the synonymous substituti

47 of G-rich oligonucleotides with an identical base composition and an increasing number of mismatches

48 These results indicate that changes in base composition and backbone insertions influence the t

49 Trends in base composition and base-pairing probabilities suggest

50 ndomly associated with regions of high G + C base composition and certain transcriptional profiles.

51 interdependence of expression patterns with base composition and chromosome structure.

52 Base composition and codon usage also conform to typical

53 analysis reveals distinctive differences in base composition and codon usage between H. glycines and

54 statistical method was used to test whether base composition and codon usage bias covary with arthro

55 , mutation dynamics are used to analyze both base composition and codon usage bias.

56 Base composition and codon usage have been detailed.

57 The extent to which base composition and codon usage vary among RNA viruses,

58 n 3 and different nucleic acids with varying base composition and conformation by using ITC (isotherm

59 substitution rate, including corrections for base composition and CpG dinucleotides, and we verify th

60 the mammalian genome owing to their GC-rich base composition and high density of CpG dinucleotides.

61 Within a defined subsequence, base composition and homodimerization values are compute

62 malian genes is highly correlated with local base composition and is therefore thought to be determin

63 way to correct rRNA for such differences in base composition and it is not possible to quantitativel

64 However, the evolutionary pattern of base composition and its potential causes have not been

65 se using models that account for the genomic base composition and length of target regions; this appr

66 than randomized mRNA sequences with the same base composition and length.

67 triplex and duplex DNA structures of similar base composition and length.

68 We find both base composition and methylation differences between the

69 erate sequences that resemble UP elements in base composition and mimic the stimulation by the rrnBP1

70 eport several relationships between flanking base composition and mutation pattern.

71 ammalian genome, which describes patterns in base composition and predicts gene distributions.

72 Intron base composition and rates and patterns of protein evolu

73 vides useful constraints on establishment of base composition and sequence and is potentially applica

74 The two introns differ significantly in base composition and substitution rate, with one intron

75 s at these sites is correlated with flanking base composition and that the A+T content of these flank

76 also revealed a possible association between base composition and vector specificity, although with b

77 on usage also strongly reflects variation in base composition and, again, AGG and TTG decrease in fre

78 structed MW spectra, and a table correlating base compositions and MS ions was compiled to handle suc

79 e identical nearest neighbors, but different base compositions and therefore different ends.

80 Masses are converted to base compositions and, by comparison against a database

81 e compounds as "POMzites" to reflect the POM-based composition and zeolitic nature of each family mem

82 ly permuted sequences of the same length and base composition, and also smaller than those of natural

83 ransition bias as well as lineage effects in base composition, and occurs more than an order of magni

84 ibonucleotide sequences of arbitrary length, base composition, and regiochemistry at the branchpoint

85 ese bands can be analyzed for the abundance, base composition, and sequence divergence of satellite f

86 rich compared to other regions of similar AT base composition, and that duplicated V1R gene blocks ar

87 Fluctuations in base composition appear to be prevalent in Drosophila an

88 This trend suggests that both sequence and base composition are important determinants of DNA duple

89 hate perturbations, which are independent of base composition, are consistent with a model of non-spe

90 le the strength of base pairing changed with base composition as expected, the strength of tertiary i

91 mplementary sequence of identical length and base composition as the (CG)(14) sequence, when the puri

92 in-coding DNA sequences has identified local base composition as the primary predictor of synonymous

93 de from these data that minor alterations in base composition at a crucial position within some, but

94 sphate backbone conformation and an averaged base composition at each residue.

95 codon usage can be considerably affected by base composition at neighboring sites.

96 sists of genes having a widely heterogeneous base composition at the third codon position.

97 report findings from comparative analysis of base composition at the whole-genome level across 2210 s

98 code the same protein but vary only in their base compositions at synonymous sites have effects on ba

99 rly when the sequences are from genomes with base compositions at the extremes of high or low G+C con

100 more of these conjugated MGBs were varied by base composition (AT- or GC-rich oligonucleotides), back

101 genomic DNA at these insertion sites-such as base composition, bendability, A-philicity, protein-indu

102 There was dependency of base composition between sites flanking the 5'-splice ju

103 However, after accounting for differences in base composition between the strands, we find no evidenc

104 The difference in base composition between two samples indicates the prese

105 at mutation bias is the major determinant of base composition bias at synonymous, intron, and flankin

106 n of Nematoda; however, long branches and/or base composition bias could be responsible for this resu

107 his enrichment cannot be simply explained by base composition bias in these regions.

108 nonymous substitution numbers to account for base composition bias.

109 tical effect, but it comes mostly from local base-composition bias and not from RNA secondary structu

110 If this base-composition bias is maintained by selection, it too

111 rtion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic

112 ter effect on detection specificity than any base-composition bias.

113 rganized into genomic islands (n = 387) with base composition biases, suggesting their acquisitions v

114 ontrol oligodeoxynucleotides having the same base composition but a different sequence did not inhibi

115 ith multiple transversions, conserving their base composition but changing their sequence.

116 quinone-modified DNA assemblies of identical base composition but different base sequence are also pr

117 ved pretraining infusions of ODN of the same base composition but in a randomized order (scrambled OD

118 ns adjacent to G213 maintained the wild-type base composition but not its sequence.

119 on (ST(m)/ST(m, infinity)) is independent of base composition but strongly dependent on the number of

120 clustered together in oligomers of identical base composition, but with different phasing relationshi

121 monly known as isochores, where a particular base composition can span millions of nucleotides.

122 Profiles consisting of product base compositions can be stored in a database, compared

123 tion experiments indicated these patterns of base composition change can emerge across mutation sites

124 Base composition changes within introns are consistent w

125 mosaic form can be observed at the levels of base composition, codon usage and gene organization.

126 A preliminary analysis of base composition, codon usage, and vector specificity in

127 ate increase can be explained by a change in base composition, codon usage, or mutation rate.

128 formation, including molecular mass, length, base composition, complete nucleotide sequence, and conf

129 analysis results, together with comparative base composition considerations, and the absence of an M

130 ith unmodified oligonucleotides of identical base composition, DEED-modified oligonucleotides were be

131 ze-dependent and base sequence-dependent (or base composition-dependent) separations.

132 ligdeoxyribonucleotide (ODN2) having similar base composition did not show any significant change in

133 election intensity, however, predicts larger base composition differences in highly biased loci.

134 l processes between species predicts greater base composition differences in neutrally evolving regio

135 d unmethylated gDNA separate based solely on base composition due to the presence of multiple C versu

136 ength sequence windows, thus eliminating the base-composition effect) the signals for noncoding RNAs

137 To test end or base composition effects, new sets of duplexes are inclu

138 election, represents the major force driving base composition evolution in Buchnera.

139 eutral mutation pressure versus selection on base composition evolution is a subject of considerable

140 We simulated base composition evolution on a phylogeny for six specie

141 Here, we study base composition evolution within the X chromosomes of D

142 By controlling for regional forces affecting base-composition evolution, this within-gene comparison

143 sts a role of natural selection in localized base composition fluctuations.

144 We first demonstrate that base composition follows the individual-strand base equa

145 surement error which provides an unambiguous base composition for a 120-mer PCR product.

146 analysis of genomic DNA revealed an unusual base composition for intron 30 and identified the mutati

147 Genomic DNA base composition (GC content) is predicted to significan

148 tructural characteristics (base pair length, base composition, gene number, gene boundaries, codon us

149 n; a scrambled oligonucleotide with the same base composition had no effect.

150 The shift in base composition has a large effect on proteins: in poly

151 decamers (four DNA and five RNA) of the same base composition has been compared by UV-melting.

152 Ubiquitous variability of the DNA base composition has the following two aspects: intragen

153 induced genes located in regions of atypical base composition has uncovered acquired genetic elements

154 This variation in genomic base compositions has long been considered to be a stric

155 We also discuss the effect of template base composition immediately downstream of the octamer p

156 onal input alone cannot produce the observed base compositions, implying a role for natural selection

157 tribution reflecting an exaggeration of this base composition in flanks relative to the gene as a who

158 ores, the strong and systematic variation of base composition in mammalian genomes.

159 conversion is unlikely to affect silent site base composition in mammals.

160 odon family, is characteristic of synonymous base composition in many species, including Drosophila,

161 bias and suggest that codon usage and genome base composition in the D. americana lineage are in appr

162 The present work provides evidence that base composition, in addition to base sequence, can infl

163 n statistical artifacts resulting from local base-composition inhomogeneity are taken into account.

164 DNA base composition is a fundamental genome feature.

165 content at synonymous sites, indicating that base composition is at mutational equilibrium.

166 Nucleotide landscapes, which are the way base composition is distributed along a genome, strongly

167 y code; and 16s rRNA, apparently because its base composition is more affected by genome-wide mutatio

168 Base composition is not uniform across the genome of Dro

169 Base composition is the least biased for any reported an

170 lationship between synonymous divergence and base composition is unclear because we find a significan

171 e hypothesis, involving selection on genomic base composition, is contradicted by the observation tha

172 from the approximately 50 kb periodicity of base composition isochores, consistent with axis associa

173 However, if the acquired DNA has an atypical base composition, it can reduce host fitness.

174 l to the wild-type-specific probe in length, base composition, location, and annealing temperature.

175 Additionally, our models reveal that local base composition (measured by GC content and density of

176 This anomalous base composition might serve as a signal to identify mac

177 hat combinatorial libraries with alternative base compositions might have innate properties different

178 The base composition near the second nicking site is also no

179 The variations did not correlate with base composition, nucleotide sequence, or internal secon

180 ines with three different DNA sequences with base composition of 100% AT, 80% AT and 100% GC in the p

181 he UL sequence contains 113,508 bp and has a base composition of 41.7% G + C.

182 ide libraries that entails extrapolating the base composition of a co-synthesized model library (dNC,

183 number of Watson-Crick hydrogen bonds on the base composition of a duplex.

184 The ability of dNC to predict the base composition of a multibase library template was cor

185 With this technique, the base composition of a PCR amplicon, less than 140 nucleo

186 Extensive variation in size, structure and base composition of alphaproteobacterial genomes has com

187 The relative base composition of DNA regulatory sequences of certain

188 The base composition of dNC was measured by HPLC.

189 mass accuracy to unambiguously determine the base composition of each amplicon (i.e., the numbers of

190 e and optical analysis, modifications to the base composition of either the loop or stem region have

191 igh gene content, forces that operate on the base composition of individual genes could help shape th

192 uggest that selection may be acting upon the base composition of isochores and large sections of junk

193 ombination of factors including the size and base composition of its constituent loops and stems.

194 ubstitutions and small indels in shaping the base composition of noncoding sequences.

195 The base composition of the 12 base library was determined b

196 native orientations depending on the precise base composition of the binding site, which also contrib

197 n abstraction and is greatly affected by the base composition of the bulge.

198 e loss from coding ends is influenced by the base composition of the coding end sequences.

199 s on the type of nucleotide cofactor and the base composition of the DNA and is centered at the hydro

200 ength of the already-displaced strand or the base composition of the DNA beyond the +2 position.

201 t is known that parsimony is biased when the base composition of the DNA sequence is skewed.

202 ine cofactor, in a manner independent of the base composition of the DNA, while the hydrolysis step o

203 A5).(dT5) tract without changing the overall base composition of the DNA.

204 , horizontally transferred genes reflect the base composition of the donor genome; but, over time, th

205 mena genes than expected by chance given the base composition of the downstream regions.

206 The length and base composition of the fragments identified indicate th

207 ncoded amino acid sequences, codon usage, or base composition of the genes examined.

208 sed at random, significantly influencing the base composition of the genome.

209 (15)N-labeled nucleosides, we determined the base composition of the genomic regions of interest.

210 or recognition of the T-arm by RUMT, but the base composition of the stem was unimportant.

211 ificant increase of G and C nucleotides, the base composition of the surveyed PAR1 introns is similar

212 duct formation toward a ratio similar to the base composition of the T4 genome.

213 investigated what contribution, if any, the base composition of the terminal redundancy made to the

214 nomic work suggests that BGC(GC) affects the base composition of yeast, invertebrate and mammalian ge

215 enotyping database was constructed using the base compositions of 65- to 100-bp sections of MLST alle

216 uld be precisely controlled by adjusting the base compositions of DNA sequences or by introducing pho

217 mononucleotide level, so that the asymmetric base compositions of exons and introns are predictive of

218 program is useful for mapping variations of base compositions of sequences, conducting studies of de

219 eated to evaluate the importance of specific base composition on aptamer binding.

220 f a positive effect of the genomic and genic base composition on mammalian gene expression.

221 The influence of local base composition on mutations in chloroplast DNA (cpDNA)

222 We addressed the question of the effect of base composition on the CspB binding to ssDNA by analyzi

223 e bottom four base-pairs to G.C (the optimal base composition) only stimulated frameshifting from 3 t

224 general property of the DNA sequence (e.g., base composition or a related feature) rather than by de

225 ow that DNA affinities depend only weakly on base composition or secondary structure, although in gen

226 not by a scrambled DNA sequence of identical base composition or the complementary sense oligonucleot

227 nterdependence between nucleotide choice and base composition over a distance of 20-1000 nt.

228 ouble-stranded DNAs of different lengths and base compositions over a range of ionic conditions.

229 ely to peaks of high local AT composition, a base composition periodicity of approximately 15 kb that

230 ted with shorter introns, as well as general base-composition preferences that likely promote spliceo

231 Genomic sequence signals - such as base composition, presence of particular motifs, or evol

232 uence evolution and (ii) a possible shift in base composition reflecting mutational bias.

233 The intron had an unusual base composition reflective of a sequence bias present i

234 y have broad implications, since silent site base composition reflects large-scale variation in G + C

235 inding is without significant preference for base composition, sequence, or the nature of DNA ends.

236 rovide novel findings that DNA structure and base composition significantly affect the yield of 8-OHd

237 cleotidic sequences characterized by diverse base compositions, sizes, and structural features, rangi

238 nd is dependent on several factors including base composition, solution concentrations, and strand le

239 t]) to the value for a polymer with the same base composition (ST(m)/ST(m, infinity)) is independent

240 Processing tasks provided by VDJPipe include base composition statistics calculation, read quality st

241 Screening programs based on these two base-composition statistics were developed.

242 ic acid as well as oligonucleotides of mixed base composition stimulated the RecA ATPase activity in

243 st dependence of polyamine binding on genome base composition suggests that sequence context plays on

244 impact being modulated, as predicted, by the base composition surrounding the first initiation codon,

245 the substrate and product molecules, and the base composition surrounding the labeling site.

246 nside Alu elements differed according to the base composition surrounding them.

247 th resulting in microsatellites of identical base composition that were not identical by descent.

248 e in defining different parameters, dose and base composition, that affect utilization of antisense o

249 and wild type, were identical in length and base composition, the amplification conditions for the d

250 The failure of DNA base composition to correlate with optimal growth temper

251 sites that differ in their central sequence base composition to test the importance of minor groove

252 R/ESI-MS) is a method that uses the amplicon base compositions to genotype bacterial species.

253 ich differ to an exceptional degree in size, base composition, transposable element content and gene

254 . mays) in relation to regional and flanking base composition using a data set of 10,472 SNPs generat

255 More intriguingly, clear separation of base-composition values calculated across polymorphic si

256 his issue in prokaryotes, the group in which base composition variation is most dramatic.

257 Using strategic changes to base composition, we identified a minimal 12-mer sequenc

258 ide and codon usage that were independent of base composition were detected in all flaviviruses, but

259 ligomers of scrambled sequence but identical base composition were ineffective, and no TFO-induced re

260 play considerable variation in their overall base compositions, which range from 13% to over 75% G+C.

261 rences, as shown by the dependence of Keq on base composition, with decreasing Keq in the order U > T

262 here is almost no strand bias with regard to base composition, with exceptions for origins of replica

263 anslocation along ssDNA is influenced by DNA base composition, with UvrD having the fastest rate alon

264 h their surroundings suggested comparing the base composition within CNEs with their 5' and 3' flanki