ライフサイエンスコーパス: base sequence

1 hanges on DNA and to recognize non-contacted base sequence.

2 re also strongly influenced by their precise base sequence.

3 NA molecule of kilobase length and specified base sequence.

4 state dynamics in DNAs having an appropriate base sequence.

5 king pattern and groove width as a result of base sequence.

6 the strands of nucleic acids depends on the base sequence.

7 ng elements due to long range effects of the base sequence.

8 lar to a typical B-DNA of similar length and base sequence.

9 otide whereas their target is defined by the base sequence.

10 DNA replication could also be influenced by base sequence.

11 ering the possibility of obtaining any given base sequence.

12 duce errors at a rate of ~0.1-1 x 10(-2) per base sequenced.

13 containing the 136 distinct tetranucleotide base sequences.

14 consisting of a single purine or alternating base sequences.

15 arying number, within PNA backbones of mixed-base sequences.

16 rs containing all 136 unique tetranucleotide base sequences.

17 ence, and a multiecho dynamic contrast agent-based sequence.

18 hips between auditory nonsense words in rule-based sequences.

19 eral models by transfer learning using Dixon-based sequences.

20 rculation by both mRNA-based and genomic DNA-based sequencing.

21 for targeted exon capture followed by array-based sequencing.

22 ouse) approach those obtained with capillary-based sequencing.

23 produce reads comparable in length to Sanger-based sequencing.

24 ith nasopharyngeal microbiota using 16S-rRNA-based sequencing.

25 iles were characterized by 16S ribosomal RNA-based sequencing.

26 , NS5A, and NS5B were detected by population-based sequencing.

27 strategy into traditional mass spectrometry-based sequencing (2D HELS MS Seq) to allow de novo seque

28 By analyzing the 1532 base sequence 5' to this TSS, using cloning and lucifera

29 The hybrids have the same base sequence [5'-GGCGCAGGCC(T/U)(T/U)CC-3'/5'-GGAAGGCC(

30 To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its larg

31 ckground distribution statistics for profile-based sequence alignment algorithms cannot be calculated

32 e, we introduce zPicture, an interactive Web-based sequence alignment and visualization tool for dyna

33 haeal sequences; it incorporates probability-based sequence alignment masks that improve the phylogen

34 Structurally based sequence alignment of DHFRs indicates the followin

35 lt for the AAV4 capsid by use of a structure-based sequence alignment of its major capsid protein, VP

36 Structure-based sequence alignment of mouse IL-6 and human IL-6 re

37 terminal subdomain and generated a structure-based sequence alignment of protein kinases in this regi

38 Structure-based sequence alignment of Rab9 with other Rab proteins

39 A structure-based sequence alignment predicts that domain 5 contains

40 Secondary-structure prediction and structure-based sequence alignment suggest that the GerBC structur

41 protein domains using a Hidden Markov Model-based sequence alignment tool (HMMer).

42 A structure-based sequence alignment was performed that predicts tha

43 Using structure-based sequence alignment, we were able to identify other

44 Structure-based sequence alignments indicate that the nine repeats

45 lly generated database of multiple structure-based sequence alignments of protein superfamilies in th

46 Structure-based sequence alignments predict this quaternary struct

47 n considered in terms of additional homology-based sequence alignments, our studies refine our unders

48 On the basis of structure-based sequence alignments, seven tRNALys anticodon varia

49 Family-based sequencing allowed us to delineate recombination s

50 another X-family polymerase, since computer-based sequence analyses of the C. elegans genome failed

51 Structure-based sequence analyses predict that the ASD defines a c

52 Structural comparisons and structure-based sequence analyses provide insights into how polyam

53 ts (MSAs) is a crucial step in most homology-based sequence analyses, which constitute an integral pa

54 A structure-based sequence analysis allowed us to identify four cata

55 Structure-based sequence analysis and phylogenic tree construction

56 MS-based sequence analysis confirmed that hpol eta catalyze

57 A structure-based sequence analysis identified 4-OD as a member of t

58 In addition, Sanger-based sequence analysis of 4,176 breakpoints at 261 SV s

59 etic assignment is achieved by automated Web-based sequence analysis of amplification products.

60 etic assignment is achieved by automated web-based sequence analysis of amplification products.

61 Single-cell PCR-based sequence analysis of B-1a, B-1b, and B-2 cell IgH

62 Structure-based sequence analysis of the AcpA superfamily predicts

63 Structure-based sequence analysis of the PutA/PRODH family led us

64 Critical to nearly any motif-based sequence analysis pipeline is the ability to scan

65 Population-based sequence analysis revealed the presence of a varia

66 Structure-based sequence analysis suggests that this interface is

67 avirus genomic sequences, accompanied by web-based sequence analysis tools.

68 accessible alternate conformations depend on base sequence and compete for occupancy.

69 PNA molecules (6-mers) with the same nucleic base sequence and different terminal groups are investig

70 sequences, and this folding is determined by base sequence and DNA context.

71 Our results clarify the interplay between base sequence and DNA superhelicity in controlling R-loo

72 to make a direct connection between the DNA base sequence and larger-scale chromatin folding.

73 igation and Cleavage (CycLiC) for contiguous base sequencing and (ii) apply it directly to a template

74 Population-based sequencing and 454 deep sequencing of NS5B gene we

75 We report a liquid-phase, capture-based sequencing and bioinformatics pipeline, Sleeping B

76 Population-based sequencing and genotyping of multiple loci demonst

77 mentation to supplement current nanoLC-MS(2)-based sequencing and identification of intact glycopepti

78 By applying mass spectroscopy-based sequencing and reverse-phase protein arrays to 547

79 of modulation can be altered by the length, base sequence, and modification state of the ssDNAs.

80 entify S. pneumoniae strains, including lytA-based sequences, and 53 sequence-specific PCRs to identi

81 otein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing in

82 he older (but much more expensive) capillary-based sequencing approach.

83 clones using costly and laborious capillary-based sequencing approaches.

84 of identical base composition but different base sequence are also probed.

85 in the distinctly different regime where DNA base sequences are chosen at random or with varying degr

86 scription factor recognition of specific DNA base sequences are well characterized and recent studies

87 ates of variant effect sizes from population-based sequencing are needed to avoid falsely predicting

88 ric linkages while maintaining the wild-type base sequence as we demonstrate for the 10-23 RNA endonu

89 Taking linker based sequences as input, iMapper scans and trims the se

90 Here, we developed a pooled-growth CRISPRi-based sequencing assay for GIs, CRISPRiSeq, which increa

91 We assessed a PCR-based sequencing assay for rapid identification of filam

92 ual of African origin using a novel ligation-based sequencing assay that enables a unique form of err

93 Using an array-based sequencing assay, we identified an autosomal-domin

94 le LightAssembler can be considered as a gap-based sequence assembler, different gap sizes result in

95 We present a detailed, BAC-based sequence assembly of the inverted human H2 haploty

96 the protein's ability to recognize contacted base sequences at positions 5-6 bases away.

97 The effects of non-nearest base sequences, beyond the nucleotides flanking a DNA le

98 as been extensively studied for a variety of base sequences, but the degree of duplex destabilization

99 We describe a novel single molecule nanopore-based sequencing by synthesis (Nano-SBS) strategy that c

100 Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, w

101 in termination sequencing and pyrosequencing-based sequencing-by-synthesis.

102 Telomeres are repetitive base sequences capping the ends of linear chromosomes, a

103 a large Swedish family was targeted by array-based sequence capture in a female diagnosed with CDA II

104 Here, we use chromatin immunoprecipitation-based sequencing (ChIP-seq) to identify 1559 and 1009 FH

105 Using chromatin immunoprecipitation-based sequencing (ChIP-seq), we demonstrated that KLLN b

106 DNAs in S. spontaneum following a similarity-based sequence clustering strategy.

107 has presented a great challenge to alignment-based sequence comparison among different virus families

108 WSeqKernel, just like any alignment-based sequence comparison method, depends on a substitut

109 computational analyses, including structure-based sequence comparison, surface matching, affinity gr

110 e pair interactions, derived by isostericity-based sequence comparisons with 3D RNA motifs from the R

111 Structure-based sequence comparisons with other AB5 toxin family m

112 -base cluster template is adjoined with a 12-base sequence complementary to the target analyte, and h

113 e-resolved genomes generated by fosmid clone-based sequencing, complemented and expanded by up to 372

114 The base sequences comprising nucleic acids provide a rich "

115 Structure-based sequence conservation analysis reveals a conserved

116 distribution of events mirrored that of four-base sequences consisting of the GG, GT, and TG dinucleo

117 losing and the stability are affected by the base sequence context and by the nature of the sugar moi

118 Base sequence context effects for each adduct are caused

119 ree extracts has been found to depend on the base sequence context in which the lesion is embedded, p

120 The influence of DNA base sequence context on the removal of a bulky benzo[a]

121 he results demonstrate that, within the same base sequence context, dA-rU base pairs are less stable

122 These effects are consistent with base sequence context-dependent differences in structura

123 To understand how this base sequence contributes to termination of transcriptio

124 tide chain primary sequence and nucleic acid base sequence, control the two-phase coexistence regime,

125 Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data

126 eful consideration in the analysis of family-based sequence data and we provided practical guidance o

127 Tests on a human diploid PCR-based sequence data set, consisting of 90,270 traces fro

128 external reference panels to analyze family-based sequence data with a small sample size.

129 However, genotype-calling methods for family-based sequence data, particularly for complex families b

130 detects and genotypes SNPs from fluorescence-based sequence data.

131 on rare variant association tests of family-based sequence data.

132 ize the pedigree information when the family-based sequencing data are available.

133 ely reveal biological phenomena from capture-based sequencing data by visualizing the normalized read

134 ifferential expression analysis of the count-based sequencing data from RNA-seq.

135 Analysis of bisulphite based sequencing data is complicated due to the convolut

136 ple was combined with dilution-amplification-based sequencing data to resolve the phase of identified

137 bitrary covariate structures from bisulphite based sequencing data.

138 genotype-phenotype relations from population-based sequence databases, which is an integral facet of

139 ution conditions for both size-dependent and base sequence-dependent (or base composition-dependent)

140 e absence of oxidants/other radicals to form base sequence-dependent intrastrand cross-links via the

141 ncies are correlated with greater extents of base sequence-dependent local untwisting and minor groov

142 s, however, render fully automated, geometry-based sequence design approaches essential for their syn

143 Finally, the cytoplasmic tyrosine-based sequence did not provide a docking site for the AP

144 or improving polymerase chain reaction (PCR)-based sequence discrimination.

145 We show that a Fourier-based sequence distance function is able to identify str

146 gressive alignment algorithm using a grammar based sequence distance particularly useful in aligning

147 hat improve the agreement with the preferred base sequence do indeed enhance the rate of protein synt

148 g reads at a rate as low as 7.6 x 10(-6) per base sequenced, dramatically improving the error rate of

149 A conserved acidic leucine-based sequence (E(160)xxxLL) within human immunodeficien

150 nowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replicati

151 We confirm that base sequence effects depend strongly not only on the sp

152 nome in vivo We have developed a novel probe-based sequence enrichment assay to sequence and analyze

153 ory with access to capillary electrophoresis-based sequencing equipment.

154 analyzing complex genomes during the Sanger-based sequencing era.

155 UAL probes, allowing identification of a one-base sequencing error in the 16S rRNA database.

156 istance (VAMPr), to (1) derive gene ortholog-based sequence features for protein variants; (2) interr

157 ate the utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chro

158 tractable as an alternative to nucleic-acid based sequencing for the multiplexed identification of r

159 Here, we detail an Illumina-based sequencing framework and bioinformatics pipeline c

160 yte structure decouples information content (base sequence) from bulk properties, such as solubility,

161 orrhoeae recognizes only DNA containing a 10-base sequence (GCCGTCTGAA) present frequently in the chr

162 The ultrashort (<100 base) sequences generated by this technology pose specif

163 -molecule, real-time sequencing and nanopore-based sequencing, have provided new opportunities for sy

164 eristics of TnpA and the lack of significant base sequence homology between targets suggested that se

165 were detected in exons 7, 11, and 21 by PCR-based sequencing; however, two variant single nucleotide

166 As in DNA, PNA strands with complementary base sequences hybridize.

167 When both base sequence identity and chemical probing reactivities

168 Single base sequences important for fliC-dependent transcriptio

169 ition by a transcription factor of a defined base sequence in a process of direct read-out.

170 by base-pair domains that vary in length and base sequence in chloroform solution by means of femtose

171 t mechanism that involves the reading of the base sequence in the DNA major groove at the binding sit

172 (wHTH) motifs use an alpha helix to read the base sequence in the major groove while inserting a beta

173 volves the specific matching with a separate base sequence in the target nucleic acid.

174 We have defined two 8-base sequences in a 39-nucleotide region in the 3'-trans

175 r, ACAP1 binds to two distinct phenylalanine-based sequences in the cytoplasmic domain of TfR that fu

176 compared SPC-sequencing with electrophoresis-based sequencing in characterizing the above BRCA1 mutat

177 Some approaches maximize the number of bases sequenced in the least amount of time, generating

178 und by WGS, were identified by viral capture-based sequencing, indicating its enhanced sensitivity an

179 Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION,

180 A 16 base sequence is the minimum for efficient hexamerizatio

181 The dominant feature of the base sequence is the proximity of the dA-rU base pair, w

182 Discrimination between non-contacted base sequences is commonly based on the differential abi

183 sent evidence to demonstrate that a tyrosine-based sequence (IVVY-255) present within the Na,K-ATPase

184 onymous variants was tested with both kernel-based (sequence kernel association test [SKAT]) and burd

185 is kernel extends an existing class of k-mer based sequence kernels, based on the recently described

186 Candidate-gene- and exome-based sequencing led to the identification of independen

187 Current web-based sequence logo analyses for studying domain-peptide

188 ponding sequence, thus implementing an index-based sequence memory storage and retrieval capability.

189 protocol and were compared against a Sanger-based sequencing method.

190 e with 454 FLX platform, the Sanger and pyro-based sequencing methodologies were complementary as eac

191 s to overcome limitations of electrophoresis-based sequencing methods.

192 mbryogenesis, and concentrated in specific 5-base sequence motifs that are CA- and CT-rich but deplet

193 panhandle structure formed by complementary base sequence of 5' and 3' ends of viral genomic RNA.

194 nsmural myocardial mechanics and the apex-to-base sequence of longitudinal and circumferential deform

195 losteric effect should be independent of the base sequence of the bound stem-loop, as observed experi

196 y are selectively synthesized by varying the base sequence of the DNA template.

197 lexible with regard to the repeat length and base sequence of the initial oligoseeds.

198 By analyzing the denaturation profiles, the base sequence of the template can be determined.

199 have a much more relaxed requirement for the base sequence of this specificity region.

200 stems, we use the information encoded in the base sequences of nucleic acids to construct three-dimen

201 The base sequences of the three 13-mers are conserved in the

202 Initially, Sanger-based sequencing of 300-400 genes thought to be relevant

203 Here, we use array-based sequencing of 62 isolates from a US national monit

204 We used 454-based sequencing of a variable region of the bacterial 1

205 ormed different mutation analyses: candidate-based sequencing of all IFT-B-encoding genes in 1,467 in

206 We performed PCR-based sequencing of one region exhibiting introgression

207 ange small subunit rRNA genes (16S rDNA) PCR-based sequencing of randomly selected clones.

208 cific microbiota, we performed 16S rRNA gene-based sequencing of retrospective tumor and matched norm

209 obial source tracking methods using amplicon-based sequencing of the 16S rRNA gene.

210 Sanger-based sequencing of the viral protein 1 (VP1) capsid reg

211 inding to two complementary DNAs, one to the base sequence on t-amide side and the other to the bases

212 the 3' end was hybridized to a complementary base sequence on the 5' end of the target.

213 conducted in order to probe the influence of base sequences on stacked (S) versus B-type (B) conforma

214 le-genome sequencing (WGS) and viral capture-based sequencing on high-grade immunohistochemically TAg

215 a double-stranded DNA molecule of specified base sequence, on which a specified level of superhelica

216 d of computational protein design as rotamer-based sequence optimization protocols have enabled accur

217 sted, mutations may not be detectable by PCR-based sequencing, or other loci may be involved.

218 lements of two ABRCs are defined in terms of base sequence, orientation, and distance from each other

219 hondrial Custom Reseq microarray as an array-based sequencing platform for rapid and high-throughput

220 ocation of DNA is a crucial step in nanopore-based sequencing platforms, where control over transloca

221 tions in parent-offspring trios from capture-based sequencing platforms.

222 By varying the base sequence preceding the uORF, we sought to vary the

223 eading approaches, (ii) deep sequence search-based sequence profile construction and (iii) a new web

224 l neural network (NN) with a local structure-based sequence profile database (LSBSP1).

225 Information from hidden Markov model-based sequence profiles and domain architecture is calib

226 Our method (Family-Based Sequencing Program, FamSeq) integrates Mendelian t

227 ethod will be useful for many ongoing family-based sequencing projects.

228 alogues of genetic variation from population-based sequencing provides an opportunity to screen for f

229 ore prevalent quality issues involve low per-base sequencing quality at the 3' end, PCR amplification

230 tric and universal method for processing per-base sequencing read count data called FIXSEQ.

231 generate billions of relatively short (~100-base) sequence reads at very low cost.

232 We present G-SQZ, a Huffman coding-based sequencing-reads-specific representation scheme th

233 Thus, DNA-based sequences reflect the state of the RNA prior to or

234 Because of their relatively relaxed base sequence requirements for target recognition, indir

235 rrelate in infants, we compared the 16S-rRNA-based sequencing results of 131 paired rectal swabs and

236 With the web-based Sequence Retrieval System (SRS) it is also possibl

237 168) of mouse homeodomains to all possible 8-base sequences, revealing rich and complex patterns of s

238 reduction), whereas a PPMO with a scrambled base sequence (scrambled PPMO) had no effect on growth.

239 Furthermore, we now provide an HMM-based sequence search that places a user-provided protei

240 e for a fixed protein backbone using rotamer based sequence search, and optimizing the backbone for a

241 Using this information and sensitive profile-based sequence searches: (1) we predict the active site,

242 ate structure as input into the optimization-based Sequence Selection to generate low potential energ

243 We have generated 36,991,173 17-base sequence "signatures" representing transcripts from

244 d on inferred homology using a statistically based sequence similarity (SIM) method, e.g. PSI-BLAST.

245 hroughput methods for single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposom

246 s was evaluated for this study using Luminex-based sequence-specific oligonucleotide typing.

247 binding site for synthetic, non-nucleic-acid-based, sequence-specific DNA-binding molecules.

248 nts demonstrated the existence of a cellular-based, sequence-specific, posttranscriptional RNA-degrad

249 come these limitations, we report a nanopore-based sequencing strategy in which short target sequence

250 es of CTCs with high fidelity using a census-based sequencing strategy.

251 Large consortium-based sequencing studies are using next-generation whole

252 Family-based sequencing studies enable researchers to identify

253 Family-based sequencing studies have unique advantages in enric

254 onsistent in an analysis of additional exome-based sequencing studies of other neurodevelopmental dis

255 y and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination o

256 sign, analysis, and interpretation of family-based sequencing studies to improve the ability to ident

257 search for Mendelian-disease genes in family-based sequencing studies, we implemented them in a cross

258 autism association in three independent trio-based sequencing studies.

259 for facilitating target discovery for family-based sequencing studies.

260 a variety of realistic parameters in family-based sequencing studies.

261 analyzed variants obtained from a population-based sequencing study of 202 genes in >14,000 individua

262 These structures demonstrate how base sequence, substituents, and drug and ion interactio

263 led into a physical map of the region by PCR-based, sequence-tagged site (STS) content mapping.

264 nant women were tested for GBS, and amplicon-based sequencing targeting the 16S ribosomal RNA V3-V4 r

265 owever, only the recent evolution in the PCR-based sequencing techniques allow the minimally invasive

266 Nanopore-based sequencing techniques can reconstruct properties o

267 A new generation of non-Sanger-based sequencing technologies has delivered on its promi

268 We report the application of single-molecule-based sequencing technology for high-throughput profilin

269 use of conventional tandem mass spectrometry-based sequencing technology--collision-activated dissoci

270 d looping-based amplification cycle (MALBAC)-based sequencing technology.

271 DNA-unwinding elements are specific base sequences that are located in the origin of DNA rep

272 context of the evolved or directed design of base sequences that give complementary pairing, duplex f

273 DNA database for short (approximately 20-30 base) sequences that will bind to a query sequence.

274 for RNA-DNA hybrid structures with the same base sequence, the opening dynamics and the stability of

275 RNA base sequence, therefore, may be sufficient to encode th

276 e molecule sequencing (SMS) platforms enable base sequences to be read directly from individual stran

277 t inhibitor of subtilisin A by an additivity-based sequence to reactivity algorithm (Laskowski algori

278 We used quantitative PCR and 16S rRNA-based sequencing to establish viral and bacterial microb

279 quid chromatography tandem mass spectroscopy based sequencing to generate a complete map of the FAP c

280 t packages DNA, without changing the primary base sequence, to establish heritable patterns of gene e

281 management approaches, including population-based sequencing, to select appropriate antiretrovirals,

282 quent gene deletion/duplication and homology-based sequence transfer events were identified within th

283 plications arise, they are prone to homology-based sequence transfers as shown by the incongruent phy

284 e, UACAUA, for RNA cleavage instead of the 5-base sequence, UACAU, for MazF-bs(arg).

285 rchaeon that cleaves RNA at a specific seven-base sequence (UUACUCA).

286 uniform across approximately 90% of targeted bases; sequence variants were called with >99% accuracy;

287 ne sequence analysis, WebGMAP provides a web-based sequence viewer with many useful functions, includ

288 sily identified retrospectively with the web-based sequence visualization tool Integrative Genomics V

289 le-exome sequencing or targeted exon-capture-based sequencing was performed on 180 tumors.

290 Sanger-based sequencing was used for mutation scanning, validat

291 The convergent, component-based sequence we present allows for rapid construction

292 tures flanking 3' ends derived from oligo-dT-based sequencing, we developed a naive Bayes classifier

293 on bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps cove

294 By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety of bacte

295 and I26 hydrophobic core positions of a GCN4-based sequence were synthesized and studied by solution-

296 NR, the SNR and confidence level with the SE-based sequences were compared with those with the GRE se

297 osine or adenine in the vicinity of extruded base sequences, were used as spectroscopic probes to exa

298 from a RNA library consisting of >10(14) 80 base sequences which differ in a 30 base randomized regi

299 y (pseudogenes) are complemented by amplicon-based sequencing with specific primers to ensure 100% co

300 hods and techniques suggest that the Tyr-255-based sequence within the NKA alpha1-subunit is the site