ライフサイエンスコーパス: sequence coverage

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

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

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

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

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

6 eater abundances of product ions and overall sequence coverage.

7 t levels of transposon insertion density and sequence coverage.

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

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

10 ying degrees of fragmentation efficiency and sequence coverage.

11 h over 900 peptides generating full backbone sequence coverage.

12 , increasing depth of proteomic analyses and sequence coverage.

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

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

15 e peptides of overlapping sequences and high sequence coverage.

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

17 dissociative charge reduction and incomplete sequence coverage.

18 t ions during CID that dramatically increase sequence coverage.

19 proteolysis) MS approach, which ensures full sequence coverage.

20 in homogenate with an average of 25% protein sequence coverage.

21 e mutation given at least 10-15-fold nominal sequence coverage.

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

23 ed in several subanalyses to further improve sequence coverage.

24 ysis of its digest, usually suffers from low sequence coverage.

25 ch CE-MS/MS subanalysis in order to maximize sequence coverage.

26 inal masses are analyzed, thereby increasing sequence coverage.

27 Operations in both directions afforded equal sequence coverage.

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

29 ore enzymatic digestion in order to increase sequence coverage.

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

31 cause CNV determination requires only sparse sequence coverage.

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

33 specific assessment of transmembrane domain sequence coverage.

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

35 cal water treatment improve reported protein sequence coverages.

36 5% of alleles in hybrid mouse cells with 30x sequencing coverage.

37 ient plasma samples with low DNA methylation sequencing coverage.

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

39 onfounding factors that significantly affect sequencing coverage.

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

41 an assemblies with only modest long molecule sequencing coverage.

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

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

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

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

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

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

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

49 We observed wide variation in sequence coverage across sites.

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

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

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

53 This high sequence coverage allowed the identification of the isof

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

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

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

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

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

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

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

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

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

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

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

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

66 The high sequence coverage and presence of mate pairs result in f

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

68 techniques are suitable, providing extensive sequence coverage and retention of the modification on b

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

70 sed proteomics is challenging owing to <100% sequence coverage and the uncoupling effect of proteolys

71 membrane and low-abundant proteins with low sequence coverage and weak signal intensity, which are o

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

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

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

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

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

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

78 MALDI-TOF mass analysis (>36% sequence coverage) and immunoblotting confirmed the iden

79 f small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy)

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

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

82 y mass spectrometry, achieved 89% amino acid sequence coverage, and identified 31 novel modification

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

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

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

86 At room temperature, very high sequence coverage (approximately 100%) was observed for

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

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

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

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

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

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

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

94 identified by 10%, but increased the overall sequence coverage by 50%.

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

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

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

98 Increasing peptide sequence coverage by tandem mass spectrometry improves c

99 Furthermore, when evaluating the protein sequence coverage by the number of distinct peptides map

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

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

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

103 However, heterogeneous sequence coverage caused by heterogeneous expression or

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

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

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

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

108 h 47-69% sequence coverage, with gaps in the sequence coverage corresponding to the carbohydrate-cont

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

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

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

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

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

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

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

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

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

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

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

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

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

122 yrosequencing technology have relied on deep sequence coverage for accurate polymorphism discovery be

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

124 ant improvement in percent fragmentation and sequence coverage for all peptides upon ETD, including f

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

126 ning CID and ETD fragmentation increased the sequence coverage for an average tryptic peptide to 92%.

127 s been observed that ECD+CID can improve the sequence coverage for beta-endorphin over performing ECD

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

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

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

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

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

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

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

135 nd surface results in a significantly better sequence coverage for singly protonated peptides than SO

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

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

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

139 With this method, we have achieved 82-99% sequence coverage for the membrane proteins carnitine pa

140 ed against a Swissprot database, the average sequence coverage for the standard I, II, and E. coli's

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

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

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

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

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

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

147 rface-modified MALDI sample probes increases sequence coverage from 61.3 to 74.5%.

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

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

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

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

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

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

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

155 hat increasing marker density yields greater sequence coverage in high LD, thus requiring more tag SN

156 at high resolution, features such as overall sequence coverage in LD blocks and block boundaries vary

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

158 approaches were explored for obtaining high sequence coverage in protein modification studies perfor

159 and z-type fragments, resulting in extensive sequence coverage in the case of triply protonated pepti

160 Factors influencing sequence coverage in the HX mass spectrometry experiment

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

162 tion of primary amines as a tool to increase sequence coverage in tryptic peptide mapping.

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

164 of the p22(phox) subunit provided 72% total sequence coverage, including assignment of the hydrophob

165 11 peptides, resulting in an average protein sequence coverage increase of 18%.

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

167 elements, the problem of obtaining adequate sequence coverage increases with the sizes of subsequenc

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

169 This list also contains protein and peptide sequence coverage information, scores, etc. that can be

170 enefit of the method is that overall protein sequence coverage is improved.

171 y of the software to cope with low levels of sequence coverage is investigated by analyzing assemblie

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

173 state there is a maximum size for which high sequence coverage is obtained and that increasing the ba

174 ation provided by both mapping methods, 100% sequence coverage is often obtained for smaller proteins

175 We demonstrate that low sequence coverage is sufficient for identifying and mapp

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

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

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

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

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

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

182 Sequence coverage might be of particular importance for

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

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

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

186 Because of the high sequence coverage obtained, the bacteriophage MS2 coat p

187 th 14 or more amino acids yielded an average sequence coverage of 23%.

188 4+), and [M + 5H](5+) ions yields amino acid sequence coverage of 42.3%, 38.5%, and 7.7%, respectivel

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

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

191 ETcaD produced a median sequence coverage of 89%-a significant improvement over

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

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

194 high separation efficiency, to increase the sequence coverage of a complex protein mixture.

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

196 ion was further extended to achieve complete sequence coverage of a therapeutic protein, recombinant

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

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

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

200 Sequence coverage of casein is interpreted showing succe

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

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

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

204 Sequence coverage of each protein digest and the number

205 The sequence coverage of each SAGE library is beyond 150K, '

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

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

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

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

210 integral membrane protein analysis, complete sequence coverage of MP20 was obtained.

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

212 In general, higher sequence coverage of peptides was obtained using IRMPD o

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

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

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

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

217 el tryptic digest samples provided 73% total sequence coverage of the gp91(phox) subunit, including t

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

219 This study reports extensive sequence coverage of the integral membrane protein Cyt b

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

221 dem MS analysis resulted in greater than 80% sequence coverage of the NTS1 protein, including all sev

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

223 surface of the elastomeric device; and (iii) sequence coverage of the peptide mass fingerprinting map

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

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

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

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

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

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

230 Very high sequence coverages of almost 80% were achieved for the h

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

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

233 in approximately 20% increase in amino acid sequence coverage over CID; and (iii) combining CID and

234 Elevated-temperature ETD provided increased sequence coverage over room-temperature experiments for

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

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

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

238 cancer genes covering 177 exons with average sequence coverage per sample of 93%.

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

240 However, low sequencing coverage presents challenges to accurate SNV

241 We address the medical sequencing coverage problem via an extension of the stan

242 Mouse Genome Sequencing Consortium, at ~7.5x sequence coverage, producing a high-quality draft assemb

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

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

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

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

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

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

249 117 gene products were identified with 100% sequence coverage revealing 26 acetylations, 1 N-termina

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

251 n of two effects contributes to the improved sequence coverage: shattering of peptide ions on surface

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

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

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

255 From the peptides studied, the ETD sequence coverage tends to be inversely related to pepti

256 otonated tryptic peptides, providing greater sequence coverage than either CID or infrared multiphoto

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

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

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

260 e subsampling of the query genome limits the sequence coverage that can be obtained and therefore red

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

262 irst complete gene sets for genomes with low-sequence coverage, the introduction of new strain variat

263 fated c'- and z.-type product ions with high sequence coverage, thereby allowing both sequencing and

264 s-C, and endoproteinase Glu-C increased this sequence coverage to 72.8%.

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

266 hese digests prior to analysis increased the sequence coverage to 97.4%.

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

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 od shows generation of tryptic peptides with sequence coverage up to 90% within minutes; trypsin auto

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

272 were identified and characterized with 100% sequence coverage via automated fragmentation of intact

273 gestion procedure was optimized, the insulin sequence coverage was 100%.

274 es composed of 8-11 amino acids, the average sequence coverage was 46%.

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

276 The sequence coverage was further enhanced by employing mult

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 95% sequence coverage was obtained by reducing human granulo

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

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

283 quely mapping reads fell within the targeted sequences; coverage was uniform across approximately 90%

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

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

286 To address this low sequence coverage, we introduce a novel technique, (CE-M

287 The sequence coverages were 48% and 22%, respectively.

288 Sequence coverages were dependent on the hydrophobicity

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

290 phorylated in wild-type mouse cTnI with full sequence coverage, which was confirmed by the lack of ph

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

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

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

294 Prokaryotic genomes do not correlate to sequence coverage, while eukaryotes show strong correlat

295 from amplified extracts, revealing unbiased sequence coverage with substantial amounts of nonredunda

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

297 TRFE was mapped with 47-69% sequence coverage, with gaps in the sequence coverage co

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