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

3 BAC displays significant biases towards high GC content.

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

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

6 ten confounded by sequencing biases, such as GC content.

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

8 reduced the bias against sequences with high GC content.

9 high recombination and low but heterogeneous GC content.

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

11 ion frequency negatively correlated with the GC content.

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

13 alyzing multiple target sequences of varying GC content.

14 of significantly reduced SNP density and low GC content.

15 RBPs and miRNAs are also biased in terms of GC content.

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

17 eferentially inserting into regions of lower GC content.

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

19 ntron length, and positively correlated with GC content.

20 e correlation between generation time and mt GC content.

21 from the focal CpG and modulated by regional GC content.

22 d for identifying genes with highly variable GC content.

23 organism with bimodal or other unusual gene GC content.

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

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

26 anslation of mRNA transcripts with low 5'UTR GC content.

27 pletely predict all grass genes with extreme GC content.

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

29 un-observed mutations in loci with variable GC-content.

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

31 allowing sequence constraints and specified GC-content.

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

33 al species with widely differing chromosomal GC contents.

34 by existing tools due to the highly variable GC contents.

35 o high or too low windowed guanine-cytosine (GC) content.

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

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

38 ence from P. longichromatophora (979,356 bp, GC-content = 38.8%, 915 predicted genes) and P. micropor

39 ed genes) and P. micropora NZ27 (977,190 bp, GC-content = 39.9%, 911 predicted genes) and compared th

40 vely promotes ribosomal interaction with low GC-content 5'UTRs.

41 ile concurrently hosting some of the highest GC contents (60.67 +/- 0.16%).

42 equence-specific binding to a region of high GC content (76%) derived from a CpG island embedded in s

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

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

45 High GC content adjacent to SINE1s is strongly correlated wit

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

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

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

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

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

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

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

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

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

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

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

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

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

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

60 Selaginella plastomes have the highest GC content and fewest genes and introns of any photosynt

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

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

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

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

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

66 % GC content and length are functional properties of intro

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

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

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

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

71 Increased GC content and number of tissues with detectable express

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

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

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

75 </= 10(-4), we examined the effect of local GC content and recombination rate on individual variant

76 We also establish GC content and ribosome footprint length as quality cont

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

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

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

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

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

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

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

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

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

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

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

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

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

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

91 RgEs varying in thermodynamic stability, GC-content and position were added to the 5'-UTR of a fl

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

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

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

95 plasmid gene content, bacterial host range, GC content, and existing classifications based on replic

96 histone modifications, nucleosome occupancy, GC content, and global 3D genome architecture.

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

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

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

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

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

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

103 s based on biological considerations-such as GC content-and applied in single samples separately.

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

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

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

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

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

109 ked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associa

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

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

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

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

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

115 rences in chromatin accessibility levels and GC contents between target and background loci in footpr

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

117 GC content bias describes the dependence between fragmen

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

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

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

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

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

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

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

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

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

127 the gold standard Kaplan model is driven by GC content (by design) and by k-mer training; for high o

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

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

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

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

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

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

134 96 synthetic RNAs with various lengths, and GC content covering a 2(20) concentration range as spike

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

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

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

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

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

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

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

142 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with

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

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

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

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

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

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

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

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

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

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

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

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

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

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

157 nomes exhibit a sharp 5 (')- 3(') decreasing GC content gradient, which is not carefully modeled by a

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

159 Salient features, including GC-content, histone modifications and Hi-C interactions

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

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

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

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

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

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

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

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

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

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

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

171 This revealed the central role of GC content in mRNA fate, in terms of P-body localization

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

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

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

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

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

177 with RNAPI distribution: folding energy and GC content in the transcription bubble.

178 Cell-essential genes had lower GC content in their 3' UTRs, suggesting a connection bet

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

180 5' end of existing genes, thus altering the GC content in those regions.

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

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

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

184 ontent increases and decreases as downstream GC content increases.

185 We show that GC content influences cell state-specific mRNA levels, a

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

187 rity, predominantly affecting short and high GC-content introns and genes involved in brain disorders

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

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

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

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

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

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

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

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

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

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

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

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

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

201 nts and ability to amplify targets with high GC content may outweigh the relatively small additional

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

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

204 HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression.

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

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

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

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

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

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

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

212 en the chromatin accessibility level and the GC content of a locus and the number and types of TF foo

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 bias is determined by the guanine-cytosine (GC) content of differentially expressed genes.

241 4 to 65%) sequences comparing to the average GC-content of 40% on chromosome 1.

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

243 ecially, SCOP employs alignment features and GC-content of paired reads to evaluate the quality of co

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

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

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

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

248 xisting methods do not control for biases in GC content or dinucleotide composition.

249 ositioned nucleosomes are often matched with GC content oscillations.

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

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

252 n reading frame length and guanine-cytosine (GC) content presents universally substantial divergence

253 capture probe count, caller concordance, and GC content providing the most discriminatory power.

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

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

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

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

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

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

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

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

262 GC content showed a quadratic relationship with genome s

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

264 gh evolutionary rates, low Guanine-Cytosine (GC) content, small genome sizes, and lower gene numbers.

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

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

267 High local GC content strongly distinguishes bound motifs from unbo

268 mized for finding genes with highly variable GC contents, such as the genes with negative GC gradient

269 size has coincided with a strong decrease in GC content - suggesting this new subclade of Synechococc

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

271 correlates with increased guanine-cytosine (GC) content, suggesting a key role for GC-biased gene co

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

287 as sequencing depth, genotyping quality, and GC contents, to predict whether a particular variant is

288 Mean bacterial genome size, GC content, total number of tRNA genes, total number of

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

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

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

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

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

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

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

300 fectively predict genes with highly variable GC contents without manual intervention.