ライフサイエンスコーパス: GC content

1 the well-studied S. pombe species (with 44% GC content).

2 ncy ( approximately 20%) irrespective of the GC content.

3 reduced the bias against sequences with high GC content.

4 high recombination and low but heterogeneous GC content.

5 orresponding to about 2.8 kilo bases of 100% GC content.

6 ns did not amplify in any sample due to high GC content.

7 alyzing multiple target sequences of varying GC content.

8 of significantly reduced SNP density and low GC content.

9 n whether the target virus has a low or high GC content.

10 eferentially inserting into regions of lower GC content.

11 igomers given the size of its genome and its GC content.

12 ntron length, and positively correlated with GC content.

13 e correlation between generation time and mt GC content.

14 f the genome with high gene density and high GC content.

15 relative to intergenic regions with similar GC content.

16 organism with bimodal or other unusual gene GC content.

17 ograms that are trained on genes with random GC content.

18 s, which span a continuous range in size and GC content.

19 pletely predict all grass genes with extreme GC content.

20 ed with genes with low exon numbers and high GC content.

21 sitivity, 11 histone modifications (HMs) and GC content.

22 BAC displays significant biases towards high GC content.

23 may actually be 'hidden' as a result of high GC content.

24 c tissues, likely due to their uniquely high GC content.

25 sampled sequences have a precise, specified GC-content.

26 UPAC constraints on RNA sequences and fixing GC-content.

27 allowing sequence constraints and specified GC-content.

28 al species with widely differing chromosomal GC contents.

29 form capture efficiency of 31 DNA molecules (GC content, 0-100%), maximized the signal difference for

30 ese young CR1s are flanked by regions of low GC content (38%).

31 led that the promoter region contains a high GC content, a non-canonical TATA box, multiple stimulati

32 ng' of genes according to properties such as GC content, a pattern search system to identify conserve

33 its less bent DNA, suggesting that increased GC content accompanies increased double helix rigidity.

34 d the most comprehensive description of gene GC content across the seed plant phylogeny so far availa

35 High GC content adjacent to SINE1s is strongly correlated wit

36 By contrast, unfavorable GC content affects gene expression at the level of the c

37 Break proximity, microhomology length and GC-content all favored repair and the pattern of MMEJ de

38 ocation, level of nucleotide divergence, and GC content, although we found no definitive evidence for

39 hat wavy signal patterns correlate best with GC content, among multiple genomic features considered.

40 rosatellite content, and L1 density, but low GC content and Alu density.

41 ental sequences through a combined effect of GC content and breadth of expression, with GC content pl

42 GC content and codon usage are the two key sequence feat

43 enome compositional evolution and exploiting GC content and codon usage frequency to identify genes w

44 sion and by determining the contributions of GC content and codon usage to gene expression efficiency

45 ave determined the relative contributions of GC content and codon usage to the efficiency of nuclear

46 ur data disentangle the relationship between GC content and codon usage, and suggest simple strategie

47 (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses

48 This score captures strong signals (GC content and conservation), as well as subtler signals

49 utionary breakpoints are further enriched in GC content and CpG islands, highlighting a potential rol

50 eal that local base composition (measured by GC content and density of L1 target sites) and natural s

51 cate retention is positively correlated with GC content and expression level; ribosomal proteins, tra

52 e properties of microbial genomes, including GC content and genome size, are known to vary widely amo

53 is critical for PcG recruitment, while high GC content and high conservation level are also importan

54 ome contains 5.1 Mb in 55 contigs with 61.2% GC content and includes a 21-gene arsenic gene island.

55 onte Carlo analyses found biases toward high GC content and intergenic and repetitive regions.

56 tified a recombination bias toward both high GC content and intergenic regions.

57 % GC content and length are functional properties of intro

58 C content, and (7) the joint distribution of GC content and length of the different domain types.

59 stance-dependent random polymer ligation and GC content and mappability bias-and model zero inflation

60 e bacterial species spanning a wide range of GC content and measured the contiguity and accuracy of t

61 n was exchanged for a new segment of similar GC content and melting temperature.

62 ns were used to examine flanking regions for GC content and nucleotide bias at the insertion site.

63 Increased GC content and number of tissues with detectable express

64 on-self-complementary duplexes with variable GC content and one of eight different DNA-interactive dr

65 may be prone to representation biases due to GC content and other factors.

66 ge along the genome suffers from bias due to GC content and other factors.

67 </= 10(-4), we examined the effect of local GC content and recombination rate on individual variant

68 res the primers based on factors such as Tm, GC content and secondary structure allowing for simplifi

69 ased on four different targets (with varying GC content and sequence features).

70 Low genome GC content and small variance in chromosome GC content a

71 ' untranslated region features revealed that GC content and the number of upstream open reading frame

72 indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation.

73 igonucleotide "words" of standard length and GC content and then amplified by PCR.

74 eproducible protocol-dependent biases due to GC content and transcript length as well as stereotypic

75 n heterochromatin, is highly correlated with GC content and transposon distribution, and may silence

76 ons are typically shorter, displaying higher GC content and weaker polypyrimidine-tracts and BPs.

77 ical amino acid sequence but differ in their GC content and/or codon usage, we show that codon usage

78 ling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separat

79 GIs had many strain-specific CDS, anomalous GC contents and/or significant dinucleotide biases, cons

80 ce length, protein length, guanine-cytosine (GC) content and triple codon counts.

81 me-wide mutational forces that shape overall GC-content and create context-dependent nucleotide bias,

82 MA), alter the usual correlation between DNA GC-content and duplex stability.

83 r-law distribution, (6) compositional domain GC content, and (7) the joint distribution of GC content

84 omoters lack TATA-like elements, have a high GC content, and are enriched in Sp1-binding sites.

85 omic hybridization, sequence factors such as GC content, and batching of samples during collection an

86 , DNA sequence identity (fraction matching), GC content, and concentration of the homologous recombin

87 ving) in part based on its small genome, low-GC content, and lack of biosynthesis pathways for most a

88 ; (iii) all sequences have identical length, GC content, and melting temperature; (iv) the identity o

89 red properties of primers, including length, GC content, and others.

90 h as localization signals, codon adaptation, GC content, and overall hydrophobicity.

91 d towards larger genome size, higher genomic GC content, and proteins with higher nitrogen but lower

92 ined correction for sequence mappability and GC content, and second, by applying this procedure to se

93 to be highly dependent on the genome length, GC content, and sequence word size.

94 We determine that GC content appears to be a significant, but not sole, fa

95 GC content and small variance in chromosome GC content are characteristic of aardvark and elephant a

96 Those 3' UTRs with a higher GC content are more likely to be associated with reduced

97 elements are found in genomic regions whose GC contents are statistically indistinguishable, and (ii

98 These regions show unusual shifts in human GC content, are unevenly distributed across both genomes

99 However, it is unclear how heterogeneity in GC content arises, and how it relates to the expression

100 lineages leading to D. yakuba and D. orena, GC content at silent sites has increased rapidly near te

101 mization of local DNA molecular dynamics via GC content at synonymous sites ( approximately GC3).

102 Many of the transcripts that have lower GC content at the third position have dicot homologs but

103 be divided into two classes according to the GC content at the third position in the amino acid encod

104 file, which correlates with the differential GC content between adjacent introns and exons.

105 Similarity of GC content between introns and flanking exons, lack of s

106 the read depth signal while considering both GC content bias and mappability bias.

107 GC content bias describes the dependence between fragmen

108 However, accounting for GC content bias in ChIP-seq is challenging because the b

109 tem largely from a failure to model fragment GC content bias.

110 We find that GC-content bias accounts for substantial variability in

111 tome-wide quantifier to correct for fragment GC-content bias, which, as we demonstrate here, substant

112 methylation entropy are associated with high GC content but depletion of CpG dinucleotides and (v) Al

113 rently occurs independently of gene size and GC content but exhibits strong preference for recently d

114 e annotations of prokaryotic genomes of high GC content but the qualitative approach of visual frame

115 Using duplex substrates with altered GC contents but similar predicted thermal stabilities, w

116 tation rate, which was correlated with local GC content, but not recombination rate.

117 re trained with grass genes with high or low GC content can make both better and unique gene predicti

118 A abundance, but by large-scale variation in GC-content, caused by meiotic recombination, via the non

119 The high GC content class is also enriched with intronless genes.

120 Variation in GC content contributes to the positioning of these seque

121 ly required, but increased flanking sequence GC content correlates with higher insertion rates.

122 that specific motifs, secondary energy, and GC content could play a role in their degradation by XRN

123 96 synthetic RNAs with various lengths, and GC content covering a 2(20) concentration range as spike

124 study the evolutionary relationships between GC content, CpG-dinucleotide content (CpGs), potential n

125 rge upstream of the TSS and independently of GC content, CpGs, and NFIs, whereas a second, weaker CG

126 icant negative GC gradient, meaning that the GC content declines along the orientation of transcripti

127 Codon bias and GC content differs among MyHC genes with regards to func

128 compositionally homogeneous domains with low GC content dispersion, whereas D(JS) failed to identify

129 ba lineage shows a less extreme elevation of GC content distributed over a wider genetic region (appr

130 te organisms, the biological significance of GC content diversity in plants remains unclear because o

131 programs trained on grass genes with random GC content do not completely predict all grass genes wit

132 ce features such as TATA-box, Initiator, and GC content do play a significant role, but many addition

133 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with

134 conversion contributed to guanine-cytosine (GC) content elevation.

135 regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift

136 low understanding the mechanisms involved in GC content evolution in plants.

137 GC content evolution is highly variable both within the

138 ent with recombination's causal influence on GC-content evolution via biased gene conversion.

139 essibility, motif scores, TF footprints, CpG/GC content, evolutionary conservation and other factors

140 Transgenes with higher GC content exhibited increased transcript and protein ac

141 terms that specifically remove biases due to GC content, exon capture and amplification efficiency, a

142 sequence-specific properties and found that GC content, folding energy, hairpin length and number, a

143 th bulk cosolute molality and increases with GC content for all N-methylated glycines, demonstrating

144 Finally, we show that GC content for each site within INE-1 sequences has evol

145 A lack of change in GC content for most introns within this region suggests

146 es with specified amino acid composition and GC content for the purpose of hypothesis testing.

147 Using flow cytometry, we report genomic GC contents for 239 species representing 70 of 78 monoco

148 These genes are characterized by low GC content, form a separate phylogenetic clade most clos

149 e between fragment count (read coverage) and GC content found in Illumina sequencing data.

150 homogeneity, unlike the regionally variable GC content found in mammals and birds.

151 dichotomy, we found continuous variations in GC content from the probably ancestral GC-poor and homog

152 The substitutions are decreasing the overall GC content (GC), at the same time making its range narro

153 exhibit diverse patterns of species-specific GC content, GC and AT skews, codon bias, and mutation bi

154 with 2000 [resp. 500] sequences of the same GC-content generated by RNAdualPF, which approximately [

155 like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinfor

156 ures of DCs usually differ for gene density, GC content, housekeeping genes, and recombination freque

157 ution of codon usage bias (CUB) and intronic GC content (iGC) in Drosophila melanogaster were based o

158 croalgal coding sequences (CDSs) with higher GC content improved transgene expression and resulted in

159 t high SINE1 density is associated with high GC content in a few long and many short spans.

160 endogenous retroviruses and genes with high GC content in alcoholics were associated with DNA hypome

161 mous substitution, and have a markedly lower GC content in coding regions.

162 There is no increase in GC content in conversion tracts compared to flanking reg

163 ere, by testing shRNAs and siRNAs of various GC content in different guide strand segments with repor

164 We provide new data on chromosome size and GC content in four Afrotherian species using flow karyot

165 nes, we found no general decreasing trend in GC content in GC-rich genes or in other genes among euth

166 d displacement synthesis is dependent on the GC content in hairpin stems and template stretching forc

167 ship with genome size, with the decreases in GC content in larger genomes possibly being a consequenc

168 In most cases, differences in GC content in metal tolerance genes and their correspond

169 g global sequence features, such as the high GC content in nucleosome-rich regions.

170 play a significant role in the evolution of GC content in plant genomes.

171 We found significantly higher GC content in smaller eccDNAs (<500 bp) than the larger

172 longer terminal inverted repeats and higher GC content in terminal and subterminal regions.

173 ene was interrupted by the breakpoint or the GC content in the 200 kB around the breakpoint had no di

174 Under DS, mRNAs with both a high GC content in the 5'-UTR and long open reading frame sho

175 ty of the point mutations and maintenance of GC content in the human genome using approximately 1.8 m

176 Messenger RNAs with low GC content in their 5' and 3'-UTRs were preferentially a

177 5' end of existing genes, thus altering the GC content in those regions.

178 served 5.8S motives, the significantly lower GC contents in at least one of three regions, and the lo

179 es need separate models based on their local GC-content in order to avoid the noise introduced to a s

180 nes, gene density and genomic features (e.g. GC content) in identifying increased or decreased chromo

181 l approach by fitting regression models with GC content included as a predictor variable, and we show

182 In intergenic regions, when the GC content increased, the frequency of changes from G or

183 rms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content.

184 The average GC content is 34.71% with 1,864 predicted ORFs, of which

185 ertheless, a statistically significant lower GC content is found only on a minority of viruses.

186 As opposed to vertebrates, evolution of GC content is less well known in plants.

187 GC content is not a reliable predictor, but the addition

188 Our results suggest that the GC content is overall not in equilibrium in the human ge

189 ination and rates of protein evolution, once GC content is taken into account.

190 On the other hand, GC-content is reduced around ACRs, excluding a major con

191 Genomic DNA base composition (GC content) is predicted to significantly affect genome

192 function Z ( *)(k) over all sequences having GC-content k, the user can require that all sampled sequ

193 and 48.9%, with several groups exceeding the GC content known for any other vascular plant group, hig

194 nvolving chromosome number and decreasing of GC content, latitudinally oriented along the AF.

195 Since the melting profile depends on the GC content, length, sequence and strand complementarity

196 which correlates with low guanine-cytosine (GC) content, limits transcription of certain genes.

197 omic distances, showing that mutation drives GC content lower in already GC-poor regions, and using o

198 y acquired genes by targeting sequences with GC content lower than the resident genome.

199 t three factors contribute to sequence bias: GC content, mappability of sequencing reads, and regiona

200 genomic adaptations associated with changing GC content might have played a significant role in the e

201 of transcription factors, guanine-cytosine (GC) content, number of GC-rich gene-rich isochores, dens

202 The high GC-content observed for the chicken leptin syntenic grou

203 orococcus MED4 has an AT-rich genome, with a GC content of 30.8%, similar to that of Saccharomyces ce

204 le circular chromosome with 919,992 bp and a GC content of 35%.

205 nome size of 606 Mbp), 221 640 contigs and a GC content of 37%.

206 e circular chromosome of 4,321,753 bp with a GC content of 44.97%.

207 of 3,015 protein-encoding genes (CDS), and a GC content of 47.7%.

208 This finding explains how a change in the GC content of a hairpin is able to influence translation

209 human genome to be AT rich and shifting the GC content of a region to approach the genome average.

210 The GC content of chordopoxvirus genomes, however, evolved i

211 decoding centre is greatly influenced by the GC content of folded structures at the mRNA entry site.

212 r genes among eutherian mammals; indeed, the GC content of GC-rich genes appears to have increased in

213 transcription factors as well as an overall GC content of greater than 60%.

214 GC content of monocots varied between 33.6% and 48.9%, w

215 d into two distinct types: those with genome GC content of more than 60% and those with a content of

216 The GC content of potato is very similar to Solanum lycopers

217 rom the catalytic center upon increasing the GC content of promoter melting region or in the presence

218 bias toward A/T, although paradoxically, the GC content of the C. reinhardtii genome is very high.

219 gene sequences generally increased with the GC content of the chromosome, while the frequency of use

220 were less biased and less influenced by the GC content of the chromosome.

221 at of TAA, was inversely proportional to the GC content of the chromosome.

222 sus promoter elements and spacer length, the GC content of the core promoter sequences had a pronounc

223 It is the GC content of the full DNA fragment, not only the sequen

224 the density of exons, long terminal repeats, GC content of the gene, and DNA methylation density in t

225 deamination activity, including changing the GC content of the genome.

226 or is a weak intrinsic terminator due to low GC content of the hairpin stem and interruptions in the

227 nversion actively maintain the heterogeneous GC content of the honey bee genome despite an overall A/

228 ical target recognition was dependent on the GC content of the miRNA seed.

229 The average GC content of the predicted coding regions of BESs is 42

230 For miRNAs with low GC content of the seed region, non-canonical targeting w

231 nts are inserted randomly, regardless of the GC content of the surrounding genomic DNA.

232 ed the existence of correlations between the GC content of the third codon position (GC(3)), methylat

233 d on their similarity to the codon usage and GC content of the tobacco plastome.

234 zer IIx is biased away from neutral to lower GC content of the transcriptomics regions.

235 The GC content of this lizard genome is also unusual in its

236 sequencing chemistry is biased toward higher GC content of transcriptome and Illumina Genome analyzer

237 um likelihood methods to infer the ancestral GC contents of 176 mammalian genes from representative e

238 ferential usage of specific codons or by the GC contents of individual chromosomes.

239 subsection of siRNA non-seed region, and the GC contents of its corresponding target sequences, are n

240 4 to 65%) sequences comparing to the average GC-content of 40% on chromosome 1.

241 depth is conditioned on the mappability and GC-content of all reads that occur at a given base posit

242 Third, the dynamics were modulated by the GC-content of the dsDNA.

243 Bacteria with higher chromosomal GC contents often contained fewer PSC trimers in their g

244 The influence of local GC content on rare variants differed from that on common

245 , excluding a major confounding influence of GC-content on the observed variation in recombination ra

246 erature T(m) at 1-2 m for DNA samples of 50% GC content or less.

247 ositioned nucleosomes are often matched with GC content oscillations.

248 f GC content and breadth of expression, with GC content playing a stronger role.

249 her fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the

250 These include regional GC content, preferential sites of fragmentation, and rea

251 Analyses of third-codon-position GC content provided conclusive evidence that the poikilo

252 Genome sizes ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the core g

253 Nevertheless, both high and low GC content regions are apparently headed towards lower G

254 Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved s

255 ning separate models for several pre-defined GC-content regions as opposed to a single model approach

256 s of interest tend to be more common in high GC-content regions, which confounds real biological sign

257 ions and scales, plotting parameters such as GC content, relative abundance, phylogenetic affiliation

258 ortant genes were often associated with high GC content, repeat elements and segmental duplications.

259 uencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis.

260 nome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associate

261 e codons were synonymously changed to reduce GC content, secondary structure, and rare codon usage.

262 e identity, free energy, continuous stretch, GC content, self-annealing, distance to the 3'-untransla

263 We also found that retained introns, high in GC content, served as substrates for the formation of tr

264 GC content showed a quadratic relationship with genome s

265 Genome GC content shows a negative correlation with size, indic

266 Probe length, melting temperature, GC content, SNP location in the probe, mutation type, an

267 We found that probe GC content, SNP position in a probe, probe coverage, and

268 High local GC content strongly distinguishes bound motifs from unbo

269 cleotide substitution reveals that the human GC content structure is out of equilibrium.

270 roach to demonstrate that the forces shaping GC content structure over the recent past (since the app

271 pecies-specific effectors had atypically low GC content, suggesting exogenous acquisition, possibly f

272 are strongly correlated with overall genomic GC content, suggesting that genome-wide mutational press

273 n bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA m

274 correlations between recombination rate and GC content, supporting both GC-biased gene conversion (B

275 lation between F(ST) estimates and the local GC content surrounding coding SNPs, suggesting that AT-r

276 us variability in the sequencing read depth: GC content, target footprint size and spacing, and repet

277 s, viral ORFans are shorter and have a lower GC content than non-ORFans.

278 ficantly smaller and had significantly lower GC content than those of the nonvaginal species.

279 re genes and have a higher guanine-cytosine (GC) content than do G-positive (R-negative) bands; howev

280 compositional domains," each with a distinct GC content that significantly differs from those of its

281 hat in photic-zone samples and with a higher GC content that suggests a distinct host and habitat com

282 analysis shows that with increasing genomic GC content the frequency of the TAA codon decreases and

283 ained on a subset of grass genes with random GC content, they are effectively being trained on two cl

284 ot a reliable predictor, but the addition of GC content to any other features enhances their predicti

285 Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain ep

286 with optional constraints, such as requiring GC-content to lie within a certain range, requiring the

287 nd for further investigation into the use of GC-content to separate data for training models in machi

288 rd position have dicot homologs but the high GC content transcripts tend to be more specific to the g

289 ect the models that explain the evolution of GC content using changes in body temperature associated

290 r DNA samples of different guanine-cytosine (GC) content using the local-bulk partitioning model.

291 forward to address the biological impact of GC content variation in microbial and vertebrate organis

292 h holocentric chromosomes, whereas increased GC content was documented in species able to grow in sea

293 careful correction for sequence identity and GC content, we predict approximately 516,000 human genom

294 Dramatic decreases in GC content were observed in species with holocentric chr

295 ons, shorter total gene length, and elevated GC content when compared with genes annotated as either

296 d length, the modelling of coverage based on GC content, whether to use real Phred base quality score

297 uenced fission yeast, S. japonicus (with 36% GC content), which is highly diverged from the well-stud

298 One aspect of gene variation is GC content, which differs across species and is bimodal

299 sequences with pre-specified amino acid and GC content, which we have developed into a python packag

300 CR1 is not inserting into regions of higher GC content within the coscoroba genome; but rather, pref