ライフサイエンスコーパス: database search

1 DAS algorithm (Metabolite Identification via Database Searching).

2 of possible decoy glycopeptides tested in a database search.

3 ntages over methods that are purely based on database search.

4 s a spectrum-adapted, a posteriori score for database search.

5 nuary 1985 and April 2012 were identified by database search.

6 ng mass spectrometry followed by appropriate database search.

7 entifications of MS/MS spectra returned by a database search.

8 s in children were identified from a MEDLINE database search.

9 protein structure prediction, and biological database search.

10 entatively matched to a peptide sequence via database search.

11 method that retains the sensitivity of pure database search.

12 tide filtration in peptide identification by database search.

13 for HCC with MR imaging were identified via database search.

14 management of chronic pain were obtained by database search.

15 of candidate peptides, thus speeding up the database search.

16 /CT for tumor staging were identified from a database search.

17 GR-Align, a CMO heuristic that is suited for database searches.

18 tive fragment ions that are reproducible for database searches.

19 and made readily accessible to many types of database searches.

20 Studies were identified by systematic database searches.

21 omain and functional predictions for protein database searches.

22 om the literature, homologous sequences, and database searches.

23 biology, especially in the context of rapid database searches.

24 ence data so as to enable successful protein database searches.

25 e, accurate mass, elemental composition, and database searches.

26 akes predictions based on iterative sequence database searches.

27 quid chromatography-tandem MS (LC-MS/MS) and database searching.

28 proach that combines de novo sequencing with database searching.

29 ndem mass spectrometry combined with protein database searching.

30 data suitable for peptide identification via database searching.

31 printing, and protein identification through database searching.

32 tide mixtures were analyzed by LC/MS/MS with database searching.

33 esulting from peptide mass fingerprint (PMF) database searching.

34 1,485 potentially relevant articles from the databases searched.

35 as a consequence of the poor indexing of the databases searched.

36 original 2326 studies identified through the database search, 38 studies were used to investigate rat

37 ts on miRNA obtained through the NCBI PubMed database search (adjusted P = 0.024).

38 modified peptide sequences was achieved by a database search against apo B-100 protein sequences usin

39 inked peptide pair using a fragment ion mass database search against known protein sequences coupled

40 manual confirmation step including a public database search against PubMed and sequence analyses, e.

41 sts of an LC-MS feature-finding algorithm, a database search algorithm, and an interactive results vi

42 ically generated peptides using a proteomics database searching algorithm.

43 e spectra at the first MSMs than an existing database-searching algorithm, MetFrag.

44 SEQUEST and X!Tandem database search algorithms were used for peptide sequenc

45 ine amino acid composition, (2) an input for database search algorithms, or (3) a basis for de novo s

46 ced dissociation (CID) MS/MS experiments and database search algorithms.

47 ine and improve peptide identifications from database search algorithms.

48 pectra of peptides that can be identified by database search algorithms.

49 need for specific parametrization of protein database search algorithms.

50 peptide tandem mass spectra identified using database searching algorithms.

51 dues for channel functions in Orai proteins, database searching also identifies a putative primordial

52 is, we present the ISPIDER Central Proteomic Database search, an integration service offering novel s

53 tal of 8199 studies were identified from the database search and 30 met the inclusion criteria for th

54 Articles were identified through a database search and by consulting reference lists of rev

55 ure alignment, multiple structure alignment, database search and clustering.

56 Database search and de novo algorithms must consider hig

57 two primary ways of analyzing MS/MS data are database search and de novo sequencing.

58 caveats associated with the use of standard database search and error-modeling methods with nonstand

59 tion of the approach based on the MassMatrix database search and LC retention time analysis programs

60 The database search and literature review failed to find an

61 on is demonstrated with test cases including database search and pairwise alignment of protein hydrop

62 The authors conducted an electronic database search and reviewed the 14 articles that fit pr

63 A total of 67 imaged lipids were assigned by database search and, in a number of cases, identified vi

64 ID INSENSITIVE1 (BRI1) is a BR receptor, and database searches and additional genomic sequencing iden

65 G) method, which performs iterative sequence database searches and annotates a query sequence with Ge

66 c reviews were identified through electronic database searches and citation tracking.

67 Studies were located via electronic database searches and hand searching.

68 ion (BioCAn), that combines the results from database searches and in silico fragmentation analyses a

69 using literature and international mutation database searches and in silico prediction models.

70 Database searches and in vitro kinase assays identified

71 provide incremental improvement in structure database searches and initial sequence database searches

72 Eligible studies were identified by PubMed database searches and other methods.

73 e data obtained from LC-MS/MS, combined with database searches and protein assembly algorithms, allow

74 eference lists to identify records missed by database searches and publicly available data not yet pu

75 pared to SPEM and HHalign, which also employ database searches and secondary structure prediction, PR

76 Third, we apply this random model to database searches and show that it surpasses conventiona

77 de) was discovered by using 3D pharmacophore database searches and was biologically confirmed as a ne

78 tial sequences derived from a combination of database searching and amino acid residue sequencing usi

79 s, these were satisfactory in relation to MS database searching and mass accuracies.

80 approaches have been established: web-based database searching and PCR-based reverse screening.

81 Here, extensive database searching and phylogenetic analysis revealed se

82 olve hard problems, such as prime factoring, database searching and quantum simulation, at the cost o

83 ion and implements improved capabilities for database searching and results filtering.

84 fied with a 99% probability using Mascot for database searching and Scaffold for assessment of protei

85 , derived based on the CDD (conserved domain database) search and literature curation.

86 spectra can be identified with conventional database-searching and protein-inference tools, allowing

87 n array of 1D/2D NMR experiments at 800 MHz, database searches, and spiking with authentic compounds

88 Rognes's SWIPE optimal database search application is still generally the faste

89 s with existing methods that employ a direct database search approach.

90 A database searching approach can be used for metabolite i

91 icted from proteins identified from an MS/MS database search are first subtracted before using the MS

92 ermediate results of sequence and structural database searches are also available.

93 Sequence database searches are an essential part of molecular bio

94 e reasonable; (ii) concatenated target-decoy database searches are preferable to separate target and

95 ation methods, including chemical similarity database searches, are limited to single or sequential l

96 A database search at 3 institutions identified all pediatr

97 Institutional database search at the Cincinnati Eye Institute revealed

98 m the United Kingdom Transplant Registry and database search at transplantation centers.

99 ategies were undertaken in July-August 2016: database searching, backwards citation searching and for

100 e search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, sp

101 dem mass spectrometry improves confidence in database search-based peptide identification and facilit

102 oid adducts were not identified in MS2-based database searches because collision-induced adduct loss

103 Medical record database searches by ICD-9 codes were used to identify H

104 ed complete eukaryotic genomes, we conducted database searching by hidden Markov models, multiple seq

105 Furthermore, "one-hit wonders" from MS/MS database searching can be further substantiated by MS in

106 To enhance the database search capabilities, the BLAST and BLAT search

107 tivities and specificities were achieved for database searches carried out with MassMatrix, Mascot an

108 A compound database search (ChemSpider) was performed to retrieve c

109 demonstrate how MSFragger empowers the open database search concept for comprehensive identification

110 Databases search consisted of MEDLINE and PubMed.

111 alk-throughs (n = 5), focus groups (n = 31), database searches, context questionnaires (n = 8), famil

112 ariants of the TDA procedure in a variety of database search contexts.

113 methods, high performance MS, and optimized database search/data filtering strategies is a powerful

114 o not use secondary structure prediction and database searches (e.g. MUMMALS, ProbCons and MAFFT), PR

115 We present a sequence database search engine that is specifically designed to

116 lementary hardware realization of a parallel database search engine that, when running on a Xilinx Vi

117 , MPA Portable now supports state-of-the-art database search engines and a convenient command line in

118 Automated database search engines are one of the fundamental engin

119 nt peptide sequence identification by common database search engines, MAGIC generates in silico spect

120 gh-throughput experiments, mass spectrometry database search engines, such as MASCOT provide a ranked

121 chlamydiae possess needle filaments, and yet database searches fail to identify a SctF homologue.

122 were systematically collected through large database searches, filtered through methodological inclu

123 A database search for "polyp" in all US examinations of th

124 A database search for EGF domain sequences shows that this

125 ins genomic integrity in this environment, a database search for genes involved in DNA repair was per

126 ntified via a pathology and dermatopathology database search for patients diagnosed as having high-ri

127 spectrometry analysis in conjunction with a database search for protein identification and semiquant

128 The approach of two-step database search for qualitative analysis and proteome to

129 A PubMed database search for relevant literature on this topic pu

130 al high throughput screening followed by web-database search for similar structures.

131 ams, and hierarchical cluster analysis), and database searching for metabolite identification.

132 r a priori spectral predictions and enhanced database searching for protein identification.

133 y analysis using high-precision instruments, database searching for the addition of N-terminal argini

134 ata and interrogate the nonredundant protein database, searching for a close match.

135 ell can be queried with a tap, and community databases searched for available information about that

136 designed queries for 4 electronic and ethics databases, searching for articles with content that was

137 FASD using multiple electronic bibliographic databases, searching for studies published up to July, 2

138 MEDLINE database searches from 1950 to 2006 were done for Englis

139 MEDLINE and Google Scholar database searches from 1966 to 2011 were performed for E

140 A database search (from January 2001 to March 2010) was pe

141 rom MS/MS spectra are identified by means of database searches, given samples with known genome-wide

142 pectrum matches (PSMs) obtained by proteomic database search has been well-recognized.

143 A human genomic database search has revealed a number of sequences conta

144 s of glycopeptide identification by a direct database search have been reported, false positives rema

145 Database searches have not been able to keep with this d

146 cture database searches and initial sequence database searches; however, the enhancements show signif

147 A Drug Gene Interaction Database search identified 47 gene products to be affect

148 An electronic database search identified 885 citations, and a manual s

149 Database searches identified 62 YY1 related sequences fr

150 PubMed and Cochrane Database searches identified articles based on design, o

151 Database searches identified five microRNAs that map to

152 Database searches identified orthologs for P19 and NEEP2

153 Systematic database searches identified studies reporting adult ADH

154 are preferable to separate target and decoy database searches; (iii) the theoretical error associate

155 ructure) retrieval algorithms, enabling full database searches in less than a second.

156 asing interest as an alternative to sequence-database searching in proteomics.

157 in scope to peptides that are identified by database searching in the first step, all MS data are co

158 Databases searched included MEDLINE, PREMEDLINE, the Coc

159 Databases searched included The Cochrane Airways Group R

160 or putatively identified based on metabolome database searches, including 20 pairs positively identif

161 Database searches indicate that the region containing th

162 Database search is the most widely used approach for pep

163 The MS/MS database search is thus reduced to extremely fast patter

164 Sequence similarity/database searching is a cornerstone of molecular biology

165 PubMed and Cochrane database searches, last conducted in December 2014, yiel

166 In traditional sequence database search, many good-quality MS/MS data remain una

167 entification rates than a prevailing reverse database searching method.

168 Although in silico database search methods remain more popular for shotgun

169 Traditional database search methods use one-against-all comparisons

170 nsistent and unified approach to de novo and database-search methods, which is a distinctive feature

171 ormance similar to that of other de novo and database-search methods, which is reasonable, given the

172 systematic reviews to identify articles the database searches might have missed.

173 of multiple sequence alignments and derived database search models, which represent protein domains

174 By identifying from a database search of approximately 15000 antibody sequence

175 Retrospective pathology database search of explant histology analysis of liver t

176 incorporating variable modifications in the database search of GlycoPep DB enhances glycopeptide cov

177 A comprehensive database search of MEDLINE, EMBASE, CINAHL, and PubMed C

178 Database search of patients from 2003-2013 who underwent

179 Database search of patients with severe limbal stem cell

180 With a radiology database search of pelvic magnetic resonance images from

181 A database search of small molecules using the quinolone 3

182 We conducted a MEDLINE/EMBASE/CENTRAL database search of studies from 1966 to May 2008.

183 Database searches of MEDLINE (PubMed), EMBASE (OVID), Co

184 We conducted electronic database searches of phase III randomized controlled tri

185 e systematically obtained through electronic database searches of PubMed/MEDLINE, PsycINFO, Web of Sc

186 jection of false positive peptide matches in database searches of shotgun proteomic experimental data

187 This outcome was especially useful for database searching of larger proteins (approximately 29

188 tein methylation sites typically starts with database searching of MS/MS spectra of proteolytic diges

189 high-throughput molecular identification via database searching of standard libraries is briefly disc

190 ransthyretin) were confidently identified by database searching of the acquired tandem spectra from p

191 of the PubMed, EMBASE, PsycINFO and Cochrane databases, search of reference lists and conference abst

192 this can be a frustrating experience because database searches often miss relevant articles.

193 regulation of OPG expression, we conducted a database search on regulatory elements in the promoter r

194 ation of intact protein species, and perform database search online to yield real-time protein identi

195 pattern sets, maximize their sensitivity in database searching or minimize the variance of the numbe

196 all phams can be assigned functions based on database searching or synteny.

197 Individual metabolites can be identified via database searching or, in the case of novel compounds, t

198 raries (CPLLs), SDS-PAGE, nLC-ESI-MS/MS, and database search, permitted identifying 175 proteins.

199 data and the identification of SAPs through database searching, post-processing and generation of HT

200 A JASPAR database search predicts that the T to C transition in r

201 The database search processor and the mass spectra processor

202 The PSI-BLAST protein database search program derives the column scores of its

203 m diagnosis software based on the MassMatrix database search program is freely available to non-comme

204 is generic and can be incorporated into any database search program to perform automated evaluation

205 ssible improvements to the PSI-BLAST protein database search program.

206 A database-searching program, Sipros 3.0, was developed fo

207 Database search programs for peptide identification by t

208 plays an important role in protein sequence database search, protein structure prediction, protein f

209 We show that, for database searching, rasbhari generates pattern sets with

210 mbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequ

211 A five-database search, reference review, and hand search ident

212 c stroke neuroprotection based on electronic database searches, references of previous publications,

213 tion of the UVPD-MS method with an in silico database search restricted to Tyr- and His-containing pe

214 ed application of the AAC information during database searching resulted in an average 3.5-fold highe

215 Since PFP and ESG are based on sequence database search results, our analyses are not only usefu

216 tage validation of primary mass spectrometry database search results.

217 The database search retrieved 4,172 unique citations, of whi

218 igned and implemented such that most protein database searches return within a few seconds.

219 A PubMed database search returned 27 studies on 16 cohorts report

220 his flavoredoxin is the only one reported, a database search revealed homologues widely distributed i

221 A transcription factor database search revealed that a putative interferon-stim

222 Database searches revealed that many members of the inte

223 Public database searches revealed that the polymorphic nature o

224 Epitope mapping and database searches revealed the presence of a structured

225 Database searching revealed that Plg-R(KT) mRNA is broad

226 lection of pairwise constraints derived from database searches, sequence similarity and user input, c

227 Database searches show p22 is structurally similar to hu

228 Database searches showed that homologs of cruF and cruG

229 Database searches showed that the genes for the glyoxyla

230 del used to rank the similarities found in a database search, so that biologically relevant relations

231 this method, independent of instrumentation, database-search software and samples, provides better es

232 omise for the development of fast structural database search solutions.

233 id composition (AAC) ions is to restrict the database search space and provide identification of pept

234 ata and a cross-validation with conventional database search strategies, we identified approximately

235 es: (i) the major assumptions made with this database search strategy are reasonable; (ii) concatenat

236 omposing a given unknown mixture, a two-step database search strategy for bottom-up nanoscale liquid

237 ass search strategy seems the most promising database search strategy.

238 he UVPD fragmentation patterns, an automated database searching strategy (based on the MassMatrix alg

239 Herein we report a novel database-search strategy based on the use of MS/MS spect

240 night tryptic digestion, sample analysis and database searching, takes approximately 24 h to complete

241 ned peptides using an ultra-tolerant Sequest database search that allows peptide matching even with m

242 Current methods use database searches that are dependent on acquiring interp

243 ns, we systematically searched peer-reviewed databases, searched the grey literature, and disseminate

244 okines of the IL-17 and IL-12 families using database searches, the factors that specify differentiat

245 n the mass spectrometer per se and following database searching, the matching of the molecular masses

246 ding time spent acquiring data, and time for database searching, the procedure takes approximately 1-

247 o the complexity of MS/MS data and the large databases searched, the accuracy of peptide identificati

248 Database searches through August 2014 identified 48 elig

249 dies (enrolling 2625 patients) identified by database searches through January 2012 were included.

250 Database searches through March 2014 were undertaken and

251 Electronic databases searched through October 2008 identified 3,794

252 etermination helps to significantly save the database search times.

253 ese pharmacophore features in small molecule database searches to identify hits with submicromolar af

254 We conducted database searches to identify members of the RNHL superf

255 strength from several sources: (i) sequence database searches to retrieve additional homologs; (ii)

256 y with isobaric tagging (iTRAQ) and multiple database searching to identify proteins that were differ

257 We present a database search tool MS-GF+ that is sensitive (it identi

258 (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST--the def

259 gene predictions, hidden Markov models, and database search tools inferring from Homo sapiens, Sacch

260 We used advanced database search tools to delineate testable hypotheses a

261 (it identifies more peptides than most other database search tools) and universal (it works well for

262 e sensitive than the three most popular pure database search tools--SEQUEST, Mascot, and X!Tandem--on

263 ovement in speed over most existing proteome database search tools.

264 ia sequences will improve the sensitivity of database search tools.

265 for x86 CPUs, most are embedded into larger database search tools.

266 tion is tandem mass spectrometry followed by database search using a program such as SEQUEST or Masco

267 8 NCBI RefSeq genomes in 33 CPU h; real-time database search using assembled or unassembled Illumina,

268 filters candidate peptide sequences during a database search using this information.

269 Protein database searches using the consensus PDZ-binding motif

270 d matrix by mass spectrometry and subsequent database searching using an O. beta transcriptomic seque

271 v2.0 was developed to perform unconstrained database searching using high-resolution tandem mass spe

272 th <10 ppm mass accuracy for highly specific database searching using tailored software.

273 In this work, we have performed database searches utilizing each D. melanogaster insulat

274 Database searching was performed by using various combin

275 ND By incorporating extensive literature and database searches, we designed a collection of TALEN con

276 Using database searches, we extracted 66 distinct human RHOGAP

277 In various database searches, we observed no new associations betwe

278 The last database searches were conducted in July 2016.

279 Database searches were conducted on October 22, 2015.

280 Online database searches were performed for studies of prostate

281 Database searches were performed using MeSH terms, keywo

282 Compound identification criteria for database searching were defined and the approach was val

283 The databases searched were MEDLINE, MEDLINE In-Process, EMB

284 Databases searched were PubMed, Cochrane Library, PsychI

285 The databases searched were PubMed, Embase (OVID version), W

286 tudies, the conventional approach involves a database search, wherein chemical shifts are assigned to

287 technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1

288 by tryptic digestion, mass spectrometry, and database searching, which we enhance using isotope label

289 ion requires roughly 1-4 h per sample, and a database search will take 0.5-2 h to complete.

290 collision-induced dissociation data into the database searches with ETD data may prove decisive in mo

291 resulting identifications while controlling database searches with robust and reproducible TDA estim

292 arily identified using biomedical literature database searches, with additional studies added at the

293 arily identified using biomedical literature database searches, with additional studies added at the

294 concept that allows one to perform an MS/MS database search without ever comparing a spectrum agains

295 The database search yielded 1303 articles, of which 139 were

296 The database search yielded 2976 articles, of which 37 were

297 A surgical database search yielded medical record numbers of 925 pa

298 A database search yielded which threshold for Banff i was

299 Database searches yielded 1923 articles, of which 257 we

300 The database searches yielded 70 trials of which 13 met thes