ライフサイエンスコーパス: sequence coverage

1 f sequence coverage (we term this "confirmed sequence coverage").

2 0.98 in 2,073 outbred laboratory mice (0.15x sequencing coverage).

3 discovery (<200 bp in 90% of cases with high sequencing coverage).

4 STRs characterized with >/=10x non-redundant sequence coverage.

5 g labile bonds, UVPD spectra provided higher sequence coverage.

6 ore enzymatic digestion in order to increase sequence coverage.

7 on (ETD) MS/MS approach obtained 80% protein sequence coverage.

8 cause CNV determination requires only sparse sequence coverage.

9 in approximately 60 s, yielding 100% peptide sequence coverage.

10 specific assessment of transmembrane domain sequence coverage.

11 d for mapping the protein sequence with high sequence coverage.

12 gest identified 37 peptides and produced 66% sequence coverage.

13 e consumption, and improves top-down protein sequence coverage.

14 g data with 500x to 2000x duplicates-removed sequence coverage.

15 and 100x Illumina whole-genome shotgun (WGS) sequence coverage.

16 eater abundances of product ions and overall sequence coverage.

17 t levels of transposon insertion density and sequence coverage.

18 hods, in addition to the increase in protein sequence coverage.

19 ing of 16S regions, but requires much higher sequence coverage.

20 ying degrees of fragmentation efficiency and sequence coverage.

21 h over 900 peptides generating full backbone sequence coverage.

22 , increasing depth of proteomic analyses and sequence coverage.

23 sis lyrata strain MN47 based on 8.3x dideoxy sequence coverage.

24 uch time, and does not always result in high sequence coverage.

25 gen/deuterium exchange for improved (78-96%) sequence coverage.

26 e peptides of overlapping sequences and high sequence coverage.

27 mina and NimbleGen-454 methods at saturating sequence coverage.

28 dissociative charge reduction and incomplete sequence coverage.

29 ches because of significantly higher protein sequence coverage.

30 ) enabled complementary proteome and protein sequence coverage.

31 e nondissociative events and thereby amplify sequence coverage.

32 on capture dissociation (ECD), yielding high sequence coverage.

33 cal water treatment improve reported protein sequence coverages.

34 an assemblies with only modest long molecule sequencing coverage.

35 arch, especially for PacBio data sets of low sequencing coverage.

36 es even in the presence of ASE and under low sequencing coverage.

37 al ancestry inference can be attained at low sequencing coverage.

38 5% of alleles in hybrid mouse cells with 30x sequencing coverage.

39 notype calling can be challenging due to low sequencing coverage.

40 onfounding factors that significantly affect sequencing coverage.

41 enerated on the Illumina GA II yielding 356x sequencing coverage.

42 alternative splicing is its reliance on high sequencing coverage.

43 ient plasma samples with low DNA methylation sequencing coverage.

44 ced using the 10X Genomics CNV solution with sequencing coverage ~0.03x, SBMClone recovers the major

45 or samples were sequenced using DOP-PCR with sequencing coverage ~0.5x, SBMClone shows that tumor cel

46 vel combination, which yields ~85% confirmed sequence coverage, 25%-30% above that from a basic prote

47 Equivalent sequence coverage (80%) is obtained with electron transf

48 We obtained high-sequence coverage (88-99%) in the HDX-MS experiments for

49 To maximize sequence coverage, a two-dimensional liquid chromatograp

50 ariations even in the presence of incomplete sequencing coverage, a known limitation of exome sequenc

51 proteome using mass spectrometry the overall sequence coverage achieved to date is still below 50%.

52 ient protease for extending the proteome and sequence coverage achieved with trypsin, with unique pos

53 We observed wide variation in sequence coverage across sites.

54 limited novel gene discovery: (1) imperfect sequencing coverage across the exome hid potentially cau

55 explore how variation in marker density and sequencing coverage affects inference.

56 digestion, we profiled, with on average 90% sequence coverage, all 13 viral proteins present in an h

57 High mass accuracy and near complete sequence coverage allowed unambiguous mapping of the maj

58 tron transfer dissociation (ETD) in terms of sequence coverage, allowing the SETA reactivity of great

59 ation of bovine serum albumin (BSA) with 19% sequence coverage and 14 peptide identifications (IDs) w

60 d signaling peptides and to provide improved sequence coverage and accurate glycosite localization, e

61 d compared their performance with respect to sequence coverage and calling of single-nucleotide varia

62 FTICR) for proteins that required additional sequence coverage and certainty of assignment.

63 ctra and substantially increases the peptide sequence coverage and confidence in peptide identificati

64 Metrics of sequence coverage and depth, quasispecies diversity, and

65 d, and the iTRAQ method provided both higher sequence coverage and enhanced signal intensity.

66 des are detected, our workflow provides full sequence coverage and even enables the identification of

67 The improvements in sequence coverage and fragment identifications are demon

68 ate and sequence intact antibodies with high sequence coverage and high sensitivity.

69 This method yields dramatically increased sequence coverage and localization of solvent-exposed se

70 stewater was retrieved with greater than 96% sequence coverage and more than 99.8% sequence identity.

71 entation event, we hypothesized that protein sequence coverage and phospho-proteoform characterizatio

72 incomplete peptide cleavages, leading to low sequence coverage and poor repeatability of analyses.

73 sed on previous work on peptides, increasing sequence coverage and PTM localization by combining sequ

74 or more disulfides and the potential gain in sequence coverage and spatial resolution would increase

75 low VAF mutations at hotspots by sufficient sequencing coverage and carefully tuned algorithms is im

76 obtain comprehensive fecal bacterial genome sequencing coverage and explore the full range of bacter

77 s including genomic objects such as genes or sequencing coverage and for web applications that requir

78 on of features, peak calling, the effects of sequencing coverage and noise, and clustering performanc

79 demonstrate a clear tradeoff between variant sequencing coverage and numbers of biological replicates

80 obtains very good performance already on 5x sequencing coverage and outperforms the fastest availabl

81 In particular, HapCUT2 scales well for high sequencing coverage and rapidly assembled haplotypes for

82 f DE, distribution of gene expression level, sequencing coverage and the choice of type I error contr

83 sis, leading to a loss of signal, inadequate sequence coverage, and a dramatic increase in the diffic

84 tides and proteins identified, total protein sequence coverage, and digestion specificity were used t

85 detected, number of peptides identified, and sequence coverage, and the digestion time was reduced to

86 ared to HCD or ETD alone, increasing protein sequence coverage, and thereby facilitating phosphosite

87 duce requirements for synthesis accuracy and sequencing coverage, and experimentally show robust data

88 or most tested combinations of tumor purity, sequencing coverage, and tree complexity, good power (>/

89 u and iTRAQ reagents show comparable protein sequence coverage (approximately 43%) and quantitation a

90 tein sequence, which can lead to a very high sequence coverage as required in typical top-down proteo

91 On-line UPLC-MS(E) generated a similar sequence coverage as the other two methods that involved

92 cleaved products, we corrected this loss of sequencing coverage at the termini by introducing modifi

93 Fragmentation efficiency/sequence coverage averaged 19/6% and 33/20% in EDD and N

94 Furthermore, we found that sequence coverage, but not variant recognition, correlat

95 The fractionation also increased the protein sequence coverage by 10-30%.

96 Our integrated approach increases sequence coverage by 7.2 percentage points and residue c

97 hydrogenase tetramer, demonstrating improved sequence coverage by combining ECD fragmentation integra

98 We propose sequence coverage by HIV Gag-specific immune responses a

99 mbined with HCD, AI-ETD improved the protein sequence coverage by more than 200% for proteins from bo

100 Increasing peptide sequence coverage by tandem mass spectrometry improves c

101 content of the target data-e.g., by reducing sequence coverage, by averaging exchange levels over lon

102 licability even in settings of extremely low sequencing coverage, by accurately imputing 5.7 million

103 that do not contain DNA residues, where high sequence coverage can be achieved by performing IT-CID o

104 horesis for protein separation with the high sequence coverage capability of microwave-assisted acid

105 However, heterogeneous sequence coverage caused by heterogeneous expression or

106 top-down proteomics is insufficient protein sequence coverage caused by incomplete protein fragmenta

107 tides in different ways to focus analysis of sequence coverage, charge state or PTMs.

108 agment ions, AI-ETD provided greater protein sequence coverage compared to both HCD and ETD.

109 the highest number of fragments and the best sequence coverage compared to pepsin or protease type XV

110 on parameters and to provide a high yield of sequence coverage compared with atmospheric pressure.

111 iform gyrus library (117 subjects) with high sequencing coverage correlated the c.2187_2188insA ADNP

112 serum albumen (BSA) more peptides and higher sequence coverage could be obtained from the protein dis

113 Both the number of peptides detected and sequence coverage decreased as the sample amount decreas

114 nterestingly, we show that increased overall sequence coverage, defined as the overall proportion of

115 s to an order of magnitude, depending on the sequence coverage depth and the position in the read.

116 particularly in the case of low-to-moderate sequence coverage depth.

117 DFinder can predict PDEs with relatively low sequencing coverage, detect multiple alternative splicin

118 Under the best conditions, the sequence coverages, determined by DESI-MS, were 100% for

119 sing just 4.7 fg of starting DNA, and obtain sequencing coverage distributions that rival that of una

120 ctrometry (LC-MS) timescale and improve mean sequence coverage dramatically (CID-only 15% vs chimeric

121 generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput.

122 b')2 mass, intact LC and Fd masses, and CDR3 sequence coverage enabled determination of heavy chain a

123 d perfectly retrieved the information from a sequencing coverage equivalent to a single tile of Illum

124 this strategy substantially improves protein sequence coverage, especially in key structural regions

125 significant increases to our structural and sequence coverage; expansion of the functional families

126 ginated from the intended target region with sequencing coverage falling within a tenfold range for a

127 atives (due to allele dropout or variance in sequence coverage), false positives (due to read errors)

128 As such, NETD improves sequence coverage, filling out the acidic portions of pr

129 approach generated more peptides and higher sequence coverage for a mixture of three standard protei

130 AI-ETD provided the greatest sequence coverage for all five charge states investigate

131 m toxin digestions has yielded near-complete sequence coverage for all seven BoNT serotypes.

132 AI-NETD achieved 100% sequence coverage for both a 6-mer (5'-rGmUrArCmUrG-3')

133 phy (LC), this LC-ECD workflow provides good sequence coverage for both trypsin and Lys C digests of

134 e NET-CID is a valuable tool to provide high sequence coverage for chemically modified oligonucleotid

135 EThcD gave the best sequence coverage for cross-linked m/z species with high

136 The method yields >95% sequence coverage for Env, provides semi-quantitative an

137 applied in parallel to provide complementary sequence coverage for large mRNAs.

138 Z (AqpZ), and surpasses previous reports of sequence coverage for mechanosensitive channel of large

139 ensive fragmentation, resulting in excellent sequence coverage for model peptide and protein cations.

140 -fold more proteins and substantially higher sequence coverage for most individual proteins.

141 s, results show that up to approximately 50% sequence coverage for selected IgG fragments is reached

142 CR mass spectrometer provides more extensive sequence coverage for structural characterization of IgG

143 ulfide bond constraints, possibly increasing sequence coverage for tandem MS analysis and yielding li

144 this technique also yields high peptide and sequence coverage for the identification of PTMs.

145 DNA residue sites and thus generated higher sequence coverage for the studied oligonucleotide.

146 deuterium content, providing almost complete sequence coverage for this 173-kDa protein.

147 the m/z range 46-13 500 showed an increased sequence coverage for three standard proteins, namely, m

148 le time-of-flight instruments and comparable sequence coverage for top-down ETD with orbitrap mass an

149 of genetic variation by providing increased sequencing coverage for genomic regions of interest.

150 emonstrate the advantages of generating high-sequencing coverage for mapping the center of discrete n

151 r high sequence similarity and heterogeneous sequencing coverage for RNA viruses.

152 large peptides (3-10 kDa) that increase the sequence coverage from 53% (2 s digestion) to 82% (0.05

153 quence reconstruction, resulting in complete sequence coverage from a single LC-MS/MS analysis.

154 orilla lineage by generating 10-fold genomic sequence coverage from a western lowland gorilla and int

155 nologies make it feasible to obtain deep DNA sequence coverage from any organism.

156 Sequence coverages from 68% to 97% were obtained for fou

157 nced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equiv

158 ymotryptic reprocessing provided significant sequence coverage gains in both soluble and hydrophobic

159 Recently, the deep sequence coverage generated by next-generation sequencin

160 xploited StcE's unique properties to improve sequence coverage, glycosite mapping, and glycoform anal

161 nucleases resulted in significantly improved sequence coverage: greater than 70% sequence coverage wa

162 The results show that high protein sequence coverages (>80%) can be obtained following subc

163 We also show that InterPro's sequence coverage has kept pace with the growth of UniPr

164 otype systems; however, very uneven (biased) sequencing coverage has been reported, which indicates i

165 le digestion (MED), primarily an increase of sequence coverage, have been reported in several studies

166 Our sequencing coverage, high-quality assemblies, and annota

167 e tiny (~9 um) microdroplets, we obtain 100% sequence coverage in less than 1 ms of digestion time, i

168 fonate retention comes at the price of lower sequence coverage in negative ion CAD.

169 ults from this study showed greater than 70% sequence coverage in the peptides identified when nonred

170 uction efficiencies, significantly enhancing sequence coverages in online coupling with MS characteri

171 The method has over 97% sequence coverage, including seven of the eight glycosyl

172 11 peptides, resulting in an average protein sequence coverage increase of 18%.

173 such as ubiquitin (8565 Da), the amino acid sequence coverage increases from 39% to 76%.

174 BSA) and HeLa cell lysate revealed excellent sequence coverage, indicating successful removal of dete

175 Although sufficient sequence coverage is critical to the success of HDXMS, i

176 in accuracy and efficiency, especially when sequence coverage is low.

177 less straightforward than for TOF MS and the sequence coverage is thus improved.

178 that ConPADE performs well as long as enough sequencing coverage is available, or the true contig plo

179 While the sequencing coverage is high enough that even rare viral

180 g accuracy and is particularly powerful when sequencing coverage is low.

181 notation, which requires Hi-C data with high sequencing coverage, is currently only available in the

182 the on-line digestion efficiency with higher sequence coverages (LC and HC >97%), thus allowing vario

183 provides confident predictions at much lower sequence coverage levels than those recommended for reli

184 al cells in parallel, but with extremely low sequencing coverage (<0.05x) per cell.

185 However, these technologies have ultra-low sequencing coverage (<0.5x per cell) which has limited t

186 Sanger sequencing and protein sequence coverage maps showed that the DNAJB9 protein de

187 cluding frequent allele dropout and variable sequence coverage may prohibit a perfect phylogeny.

188 Sequence coverage might be of particular importance for

189 older sequencing methods and obtain the high sequence coverage needed to detect rare genetic variants

190 We compare the sequence coverage obtained with 2D ECD FT-ICR MS with th

191 rage obtained with 2D ECD FT-ICR MS with the sequence coverage obtained with ECD MS/MS and compare th

192 ehensive view of transporter dynamics (85.8% sequence coverage) occurring throughout the multidrug ef

193 utic antibody trastuzumab (~148 kDa), with a sequence coverage of 100% for light chains and 85% for h

194 4+), and [M + 5H](5+) ions yields amino acid sequence coverage of 42.3%, 38.5%, and 7.7%, respectivel

195 he reference proteome, with a median protein sequence coverage of 51%.

196 This method resulted in an observed sequence coverage of 79% for cytochrome C (eight peptide

197 agmentation efficiency of 69% and an average sequence coverage of 82% with complete sulfonate retenti

198 timized workflow also enabled a similar high sequence coverage of 96% and 87% for the heavy and light

199 ique peptides were identified with a protein sequence coverage of 99 +/- 1%.

200 ins of bovine origin (Bos genus) and a large sequence coverage of a plant protein charybdin (Charybdi

201 t urea was beneficial, resulting in improved sequence coverage of all membrane proteins, in contrast

202 er with or without the copper, resulted in a sequence coverage of approximately 50%.

203 Overall quality of spectra, as judged by sequence coverage of both peptides, is best for EThcD fo

204 hermore, we obtained a significant amount of sequence coverage of both the constant and variable regi

205 Sequence coverage of casein is interpreted showing succe

206 ir collision energies with regard to optimal sequence coverage of cross-linked peptides.

207 UVPD yielded over 80% sequence coverage of DHFR and resulted in production of

208 (i) The high sequence coverage of DXPS allowed us to monitor structur

209 Sequence coverage of each protein digest and the number

210 reas the phenol method provided the greatest sequence coverage of identified proteins.

211 ted collision energy dependence of confirmed sequence coverage of individual peptides and full protei

212 g sample losses and maximizing MS-detectable sequence coverage of individual proteins.

213 ation and has proven effective in increasing sequence coverage of intact proteins.

214 er extension steps to rapidly enable uniform sequence coverage of long contiguous sequence targets in

215 provements clearly improve the detection and sequence coverage of middle-range peptides and should gu

216 Complete sequence coverage of monospecific antibodies was previou

217 ed, and the optimized workflow increased the sequence coverage of NGF from 46% with chemical reductio

218 haea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space.

219 ture HDX-MS offers the potential to increase sequence coverage of proteins being analyzed through mas

220 and which potentially contribute to gaps in sequence coverage of proteins.

221 In each experiment, we have obtained >98.7% sequence coverage of SsoMCM from >650 peptides (5-30 res

222 With this approach, 100% sequence coverage of the hemagglutinin sample was obtain

223 UVPD provides excellent sequence coverage of the larger peptides that are often

224 e and glycan product ions that afforded 100% sequence coverage of the peptide and glycan moieties fro

225 ved phosphomapping, the method increases the sequence coverage of the proteins identified, thereby in

226 Using this approach, we obtained 100% sequence coverage of the total antibody in a single chro

227 PD-NGS) that allows up to 10,000-fold deeper sequence coverage of the typical six- to eight-residue p

228 e generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtK

229 photoincorporation were observed despite 90% sequence coverage of the whole beta3 subunit protein, in

230 Both NETD and AI-NETD afforded complete sequence coverage of these molecules while maintaining a

231 f additional hydrophobic proteins and better sequence coverage of TMD-containing proteins in plasma m

232 ungulate, we obtain approximately 90% direct sequence coverage of type I collagen alpha1- and alpha2-

233 ilation of these MS/MS methods leads to high sequence coverages of 60-80% for each subunit of the ADC

234 brid MS-CID-IM-MS approach yields amino acid sequence coverages of 84.6%, 65.4%, and 69.2%, respectiv

235 mAb includes two desalting steps and showed sequence coverages of 95-100%.

236 We first demonstrate that the sequencing coverage of mtDNA in ChIP-seq experiments is

237 A new study demonstrates that genomic sequencing coverage of plasma DNA fragments around trans

238 lso investigate the effects of file size and sequencing coverage on successful file retrieval and loo

239 lative biomass of the targeted specimens and sequencing coverage on taxon recovery.

240 ice from 5 ng of total DNA yielded excellent sequence coverage over the entire bacterial genome, with

241 roduced during sample preparation, increased sequence coverage per liquid chromatography (LC) MS expe

242 ffort, marker density is more important than sequence coverage per marker in terms of the amount of g

243 In addition to full sequence coverages, posttranslational modifications (PTM

244 However, low sequencing coverage presents challenges to accurate SNV

245 Seq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates i

246 loci accurately from simulated data with 40x sequence coverage quickly while the other programs showe

247 on and insert length (for paired-end reads), sequencing coverage, read alignment and k-mer frequency.

248 ates into recoverable sequences, and 30-fold sequence coverage recovers most of these template sequen

249 -source fragmentation, resulting in complete sequence coverage regardless of the amino acid compositi

250 In order to achieve the full sequence coverage requested for reliable decoding, the s

251 nological advances, intrinsic noise and high sequence coverage requirements greatly limit the applica

252 rotein sequence is difficult, and incomplete sequence coverage results in uncertainty in distinguishi

253 Additionally, sequence coverage serves as a valuable measure by which

254 ermodynamic properties; and (iii) the target sequence coverage should be homogeneous and avoid signif

255 In summary, variation in deep sequencing coverage simultaneously shows the size, locat

256 del peptides and show that informative, high-sequence-coverage spectra are readily attainable with th

257 the protein backbone and consequently higher sequence coverage than HCD.

258 ng of an unknown cyclotide with much greater sequence coverage than that obtained with a conventional

259 droplets can yield reasonably higher peptide sequence coverage than unheated droplets.

260 NA demonstrated strikingly lower whole-exome sequencing coverage than DNA from fresh blood draw.

261 tion of SNP-trait associations at much lower sequencing coverage than the current methods, leading to

262 cal issues, such as the level of Neanderthal sequence coverage that can realistically be obtained fro

263 S(3) analysis using HCD or CID increased the sequence coverage to 89%.

264 ical coverage, and that LI-WGS requires less sequence coverage to detect a heterozygous event with a

265 ces matching with >95% sequence identity and sequence coverage to the manually curated sequences than

266 ent protein complexes, leading to comparable sequence coverage to what was achieved using the instrum

267 SA-Seq data analysis require relatively high sequencing coverage to detect significant single nucleot

268 and 6 controls) of 13 samples had sufficient sequencing coverage to yield the whole genome for HPIV3,

269 an index of replication (iRep) based on the sequencing coverage trend that results from bi-direction

270 Sequence coverages up to 80% were achieved for carbonic

271 Comparison of sequence coverages upon UV photoactivation of HA and of

272 timized instrument parameters to obtain high sequence coverage using a synthetic standard peptide.

273 To further improve sequence coverage values, a multistage MS/MS approach is

274 Full sequence coverage was achieved for each protein, and six

275 improved sequence coverage: greater than 70% sequence coverage was achieved on mRNAs near 3000 nucleo

276 The average sequence coverage was found to be higher for EThcD (28%)

277 Consequently, protein sequence coverage was increased by 20-30%, on average, a

278 Adequate sequence coverage was not recovered for the third case.

279 igh quality of MS/MS spectra leading to high sequence coverage was observed.

280 picua, where, in each case, greater than 93% sequence coverage was observed.

281 95% sequence coverage was obtained by reducing human granulo

282 tamate dehydrogenase (56 kDa), and up to 74% sequence coverage was obtained for 25 kDa antibody drug

283 s for this membrane protein, better than 89% sequence coverage was obtained for the receptor.

284 Extensive sequence coverage was obtained from the middle-down anal

285 As a result, sequence coverage was significantly enhanced, as exempli

286 Median sequencing coverage was 675x using a MinION flow cell an

287 orous, industrially acceptable definition of sequence coverage (we term this "confirmed sequence cove

288 able conditions of nucleotide conversion and sequence coverage, we can accurately count the number of

289 databases; this result suggests that at this sequence coverage, we can detect most of the known genes

290 Furthermore, significant improvements in sequence coverage were achieved by tailoring the chromat

291 Sequence coverages were dependent on the hydrophobicity

292 es to trypsin for protein identification and sequence coverage when applied to S. pombe whole cell ly

293 wever, because ETD only yields comprehensive sequence coverage when the charge state of the precursor

294 paration, providing high peptide and protein sequence coverage while allowing precise mapping of PTM

295 s in AI-ETD+ substantially increases peptide sequence coverage while also improving peptide identific

296 s a viable means to achieve in-depth protein sequence coverage while maintaining a high rate of data

297 gle antibody include: (i) extensive antibody sequence coverage with up to 100% for the light chain an

298 nables reaching only up to approximately 30% sequence coverage, with incomplete sequencing of the com

299 Due to the high sequence coverage within each sample, the frequencies of

300 d and have suggested that achieving complete sequence coverage would be a valuable attribute of a nex