ライフサイエンスコーパス: sequence database

1 nd the UniProt Metagenomic and Environmental Sequence Database.

2 nd the UniProt Metagenomic and Environmental Sequence Database.

3 el genes with no homologs in current protein sequence database.

4 d unidentified organisms present in the NCBI sequence database.

5 p records found in the Genbank Genome Survey Sequence database.

6 hieve this level of coverage for the current sequence database.

7 ndicated near complete coverage of the viral sequence database.

8 cted to a single genome or across the entire sequence database.

9 between peptide MS/MS spectra and a protein sequence database.

10 using the Los Alamos National Laboratory HIV sequence database.

11 tory of over 85% of all architectures in the sequence database.

12 ectrometry coupled to searching of a protein sequence database.

13 , and among recombinant sequences in the HIV Sequence Database.

14 in homology detection searches over a large sequence database.

15 comparing tandem mass spectra with a protein sequence database.

16 ar modules found in the nonredundant protein sequence database.

17 d model spectra generated from peptides in a sequence database.

18 from the baboon STLV-1 sequence in the NCBI sequence database.

19 his information to build a new non-redundant sequence database.

20 a 50% increase in the size of the underlying sequence database.

21 that is created based on the target protein sequence database.

22 ion about gene structure extracted from cDNA sequence databases.

23 the number of matches found by comparison to sequence databases.

24 of Type I and Type II systems within current sequence databases.

25 for the source organisms represented in the sequence databases.

26 resented by the cultured viruses in existing sequence databases.

27 sented in the INSDC's nucleotide and protein sequence databases.

28 nce clustering analyses is present in public sequence databases.

29 n contained in the rapidly expanding protein sequence databases.

30 ous information for it from existing protein sequence databases.

31 is stored in the scientific literature or in sequence databases.

32 ntains the putative R-M systems found in the sequence databases.

33 eful for screening new submissions to public sequence databases.

34 tified using BLASTx searches against protein sequence databases.

35 ns usually misidentified and misannotated in sequence databases.

36 etoheptane-1,7-dioate aldolase (HpcH) in the sequence databases.

37 e pruning, taxonomic profiling and reference sequence databases.

38 ped to x-ray crystallographic structures and sequence databases.

39 ing for sporadic selenocysteine-Cys pairs in sequence databases.

40 feasible, due to the rapid growth of public sequence databases.

41 d range of taxa, including those lacking any sequence databases.

42 hen determined with the use of public genome sequence databases.

43 show little similarity to other genes in the sequence databases.

44 on-coding RNAs and in the validation of gene sequence databases.

45 enzymes in this pathway were identified from sequence databases.

46 to all chloroplast genomes available in the sequence databases.

47 s have no close match with other peptides in sequence databases.

48 ides from tandem mass spectra and amino acid sequence databases.

49 al SECIS elements and selenoprotein genes in sequence databases.

50 nse regulators that can be identified in the sequence databases.

51 n a query sequence and entries in nucleotide sequence databases.

52 e often mis-annotated as functional genes in sequence databases.

53 s examined through mining of EST and genomic sequence databases.

54 in ASAP based on sequence similarity to five sequence databases.

55 ies have led to the expenential growh of the sequence databases.

56 e it applicable to the management of protein sequence databases.

57 C gene product did not match anything in the sequence databases.

58 nce similarity searches of GenBank and other sequence databases.

59 ch regions that have poor coverage in genome sequence databases.

60 r screening against all endogenous reference sequence databases.

61 function discovery in the rapidly expanding sequence databases.

62 th cancer can be detected by searching tumor sequence databases.

63 d whole-exome sequencing (WXS) data to viral sequence databases.

64 y of accurately identifying viruses in human sequence databases.

65 various lengths against cDNA and/or genomic sequence databases.

66 ethods with nonstandard data sets and custom sequence databases.

67 es for building and using customized protein sequence databases.

68 otations rarely get incorporated into public sequence databases.

69 ecent years has led to the creation of large sequence databases.

70 ndex the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an

71 tegrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping,

72 tegrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping,

73 tegrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping,

74 tegrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping,

75 statistical limits of the PPI structure and sequence databases, amino acid-specific pseudocounts wer

76 A sequence database analysis revealed that 92.9% of HIV-1

77 ates provides access to a manually annotated sequence database and a database of immunological epitop

78 spectrum against a combination of a protein sequence database and a spectral library.

79 between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleot

80 g the 300-kb deletion using the human genome sequence database and confirmed the map using various ST

81 ontained in the Stanford HIV RT and Protease Sequence Database and have specific usefulness.

82 Using subcellular fractionation, an improved sequence database and MS we determined the composition,

83 the usefulness of SmartGene IDNS, a 16S rRNA sequence database and software program for microbial ide

84 rchive (ENA), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has ide

85 data, including the GenBank(R) nucleic acid sequence database and the PubMed database of citations a

86 use and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the

87 Using the Los Alamos HIV sequence database and the UK HIV drug resistance databas

88 Using the Los Alamos HIV sequence database and the UK HIV drug resistance databas

89 metagenomics has led to the rapid growth of sequence databases and enabled a new branch of microbiol

90 gularly updated versions of the main protein sequence databases and is backed up by significant compu

91 With the rapid progress in sequence databases and machine-learning techniques, it i

92 Large sequence databases and new fast phylogenetic software al

93 gularly exchanges data with all major fungal sequence databases and other community resources.

94 s the gap between biodiversity repositories, sequence databases and research results.

95 uses CMs to search for new family members in sequence databases and to create potentially large multi

96 e utility of BLAST to query against multiple sequence databases and user sequence datasets, and provi

97 WspA has no similarity to entries in the sequence databases and wspA, a possible xenolog, is rest

98 Here, we interrogated a comprehensive RNA-sequencing database and found that human RMS diffusely d

99 quence were selected from the Los Alamos HIV Sequence Database, and a phylogenetic tree was created o

100 ce alignment or profile HMM against a target sequence database, and for searching a protein sequence

101 ARBitrator rapidly updates a public nifH sequence database, and we show that it can be adapted fo

102 technology costs, expanding curated pathogen sequence databases, and better data analysis tools, ther

103 two classes, MgDb for working with 16S rRNA sequence databases, and mgFeatures for marker-gene surve

104 , studies utilize different 16S primer sets, sequence databases, and parameters for sample and databa

105 NA Families Database or annotated in genomic sequences databases, and their phylogenetic distribution

106 Profile searches of sequence databases are a sensitive way to detect sequenc

107 Biological sequence databases are integral to efforts to characteri

108 Protein sequence databases are the pillar upon which modern prot

109 Genomic sequence databases are useful tools to identify conserve

110 lished that despite the annotation of PDP in sequence databases as carboxyphosphoenolpyruvate mutase,

111 ORFan genes, which have no homologues in the sequence databases, as well as the creation of genes de

112 The EMBL Nucleotide Sequence Database at the EMBL European Bioinformatics In

113 g sensitive local and global search of large sequence databases at exceptionally high speeds.

114 rated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Instit

115 he most comprehensive, non-redundant protein sequence database available.

116 deposited into the Bacterial Isolate Genome Sequencing Database (BIGSdb).

117 Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on seque

118 similarity relationships among proteins in a sequence database by performing a diffusion operation on

119 xhaustive screening of Plasmodium sp. genome sequence databases by using COWP genes as BLAST queries

120 bacterial species indicate that existing DNA sequence databases carry only a tiny fraction of the tot

121 ta submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combin

122 the members of the International Nucleotide Sequence Database collaboration (INSDC) describe each of

123 repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the

124 Under the International Nucleotide Sequence Database Collaboration (INSDC), globally compre

125 is operated by the International Nucleotide Sequence Database Collaboration (INSDC).

126 The International Nucleotide Sequence Database Collaboration comprises three global p

127 The members of the International Nucleotide Sequence Database Collaboration set out to capture, pres

128 h in analogy to the International Nucleotide Sequence Database Collaboration, aims to provide interna

129 ata archived by the International Nucleotide Sequence Database Collaboration.

130 compliance with the International Nucleotide Sequence Database Collaboration.

131 ee partners of the International Nucleotides Sequencing Database Collaboration (INSDC) (Cochrane G, e

132 The partners of the International Nucleotide Sequencing Database Collaboration, which includes the Na

133 The HCV sequence database collects and annotates sequence data a

134 The HCV sequence database collects and annotates sequence data,

135 The HFV sequence database collects and stores sequence data and

136 .Q184R)] in 14 families from our whole exome sequencing database composed of 1385 patients with inher

137 the rapid changes in size and composition of sequence databases, conservation calculations must be re

138 epitope variability in the Los Alamos HIV-1 Sequence Database, consistent with TCR evolution being d

139 ly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly re

140 e elements is a promising, low-cost means of sequence database curation and annotation.

141 addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic path

142 iterative scanning and alignment of a large sequence database during which a scoring profile is prog

143 gn long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gig

144 nitially annotated "hypothetical protein" in sequence databases, exhibits an acyl-coenzyme A (acyl-Co

145 om 76% to 87%, and can be used to filter the sequence database for identifying truncated peptides.

146 e analysis pipeline is the ability to scan a sequence database for occurrences of a given motif descr

147 n sequences and subsequently queries the PDB sequence database for the best matches, scans for possib

148 for a protein, the new server will search a sequence database for the closest homolog with an availa

149 , and we evaluate the suitability of current sequence databases for forensic and epidemiological inve

150 (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new

151 By screening sequence databases for potential peptides, we then recon

152 es of zebrafish EST and whole genome shotgun sequence databases for sequences encoding the sterol-sen

153 rehensive and scalable alternative to native sequence databases for similarity searches and reinforce

154 reported that searches of transcript and DNA sequence databases for wheat and other cereals failed to

155 d extracts all amplicon sequences in a large sequence database from a list of primers and probes, all

156 Sequence databases from across the phylogenetic tree are

157 The rapidly accumulating protein sequence databases from genome, metagenome and microbiom

158 This result suggests that well developed sequence databases from model plants like Arabidopsis th

159 generation of customized, annotated protein sequence databases from RNA-Seq data; and (ii) accurate

160 The extensive metagenomic sequence databases from the Global Ocean Sampling Expedi

161 load of disruptive mutations in whole-exome sequence databases from two cohorts.

162 n of two of the most prominent cancer genome sequencing databases from different institutes (Cancer C

163 l peptides (not present in reference protein sequence databases) from mass spectrometry-based proteom

164 tified by detailed bioinformatic analysis of sequence databases, function was investigated both by RN

165 try combined with a sample-specific antibody sequence database generated by high-throughput sequencin

166 In this approach, customized protein sequence databases generated using genomic and transcrip

167 As the size of bio-sequence databases grows exponentially, the computationa

168 The size of the protein sequence database has been exponentially increasing due

169 The availability of bacterial genome sequence databases has facilitated the identification of

170 The exponential growth of protein sequence databases has increasingly made the fundamental

171 Public gene sequence databases have become important research tools

172 Comparisons within expanding sequence databases have revealed a dynamic interplay amo

173 Analysis of increasingly saturated sequence databases have shown that gene family sizes are

174 in animals, interrogation of animal protein sequence databases identified candidates that exhibited

175 pean Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Jap

176 These methods replace the reference sequence database in proteomic database searching with a

177 the sequences of the genes in the Reference Sequence database in these samples.

178 y ion mass spectra are compared with protein sequence databases in order to identify the amino acid s

179 , the tools will enhance the value of genome sequence databases in support of integrated paleogenomic

180 Protein sequence databases include UniProtKB, InterPro and Pfam,

181 tectable in other species represented in the sequence databases, including 19 other mammals with draf

182 Analysis of rice genome sequence database indicated the presence of 3 additional

183 ntologies and a fully-structured markers and sequences database integrated with genome browsers and m

184 tributed daily and the whole EMBL Nucleotide Sequence Database is released four times a year.

185 Misannotation in sequence databases is an important obstacle for automate

186 ing these names to the associated entries in sequence databases is becoming increasingly important fo

187 ch means that a lot of information in public sequence databases is not linked to formal taxonomic nam

188 quence homology from genomic and metagenomic sequence databases is straightforward, prediction of cor

189 nsembl Trace Archive and the EMBL Nucleotide Sequence Database, known together as the European Nucleo

190 tion of structural databases such as MSD and sequence databases like UniProt is the absence of up to

191 ot rely on alignment, assembly and reference sequence databases; making it fast and scalable for larg

192 The continued growth of the target sequence databases means that traditional tabular repres

193 Using a computational sequence database mining approach, we identify two class

194 Due to growth in the sequence databases, multiple sequence alignments can oft

195 strands and the absence of the mutation from sequence databases, normal adjacent tissues, and other c

196 Current sequence databases now contain numerous whole genome seq

197 findings, we screened our ADV clinical-study sequence database of 853 patients and identified 4 who,

198 66 were identified in a large (>600 strains) sequence database of fimH-positive E. coli strains.

199 analysis strategy and apply it to a curated sequence database of hundreds of protein families.

200 Using the coding sequence database of Sorghum bicolor, 6,809 BESs found h

201 esult of bioinformatic screening of the gene sequence database of the parasitic protozoan Leishmania

202 Whole-genome sequence databases offer new in silico approaches for de

203 he contained modules allow for formatting of sequence databases, peptide spectrum matching, statistic

204 Similar to no other proteins in sequence databases, PlyC defines a previously uncharacte

205 The exponential growth of sequence databases poses a major challenge to bioinforma

206 Most major genome projects and sequence databases provide a GO annotation of their data

207 of diverse confident homologs in the current sequence databases provide an increased quality of simil

208 The rapidly expanding genomic sequence database provides a good opportunity to study g

209 ds submitted to the International Nucleotide Sequence Database public archives.

210 ceeded to extract information from unlabeled sequence databases relevant for various protein predicti

211 y database, PlantCyc, and a reference enzyme sequence database, RESD, for annotating metabolic functi

212 closely related variant from curation of the sequence database resulted in a native-like dimeric TIM

213 ST screening of the Toxoplasma gondii genome sequence database resulted in identification of a gene e

214 AST screening of a complete C. parvum genome sequence database resulted in identification of eight ad

215 oinformatics and molecular modelling to mine sequence databases, resulting in a diverse panel of enzy

216 Genetic sequence database retrieval benchmarks play an essential

217 Genomic sequence databases reveal the widespread occurrence of m

218 Alignment of hydrogenase sequences from sequence databases revealed many rare substitutions; the

219 A survey of sequence databases revealed that homologs of DES are wid

220 Informatic interrogation of mRNA sequence databases revealed upregulation of the eIF5A-PE

221 An in silico survey of viral sequence databases reveals that most positive-strand and

222 past year include a new PubMed interface, a sequence database search and a gene orthologs page.

223 We present a sequence database search engine that is specifically des

224 Protein sequence database search programs may be evaluated both

225 Since PFP and ESG are based on sequence database search results, our analyses are not o

226 In traditional sequence database search, many good-quality MS/MS data r

227 It plays an important role in protein sequence database search, protein structure prediction,

228 ough its web interfaces for analyses such as sequence database search, statistical validation, and qu

229 the past year include PubMed Labs and a new sequence database search.

230 group (ESG) method, which performs iterative sequence database searches and annotates a query sequenc

231 Sequence database searches are an essential part of mole

232 -gel proteolysis, peptide mapping by MS, and sequence database searches for protein identification, w

233 Genomic sequence database searches reveal its localization to th

234 rives its strength from several sources: (i) sequence database searches to retrieve additional homolo

235 hm that makes predictions based on iterative sequence database searches.

236 t in structure database searches and initial sequence database searches; however, the enhancements sh

237 ation (Apollo), data mining (BovineMine) and sequence database searching (BLAST).

238 itive and false negative sequence matches in sequence database searching of tandem mass spectrometry

239 ion of peptides and proteins heavily rely on sequence database searching or spectral library matching

240 on with peptide match probability scoring in sequence database searching.

241 hy electrospray tandem mass spectrometry and sequence database searching.

242 awn increasing interest as an alternative to sequence-database searching in proteomics.

243 eed-up is independent of the size of growing sequence databases, SeqVec provides a highly scalable ap

244 gainst the germline gene databases and other sequence databases simultaneously to minimize the chance

245 The performance gap grows as sequence database size increases.

246 f analyses in the face of increasing protein sequence database size.

247 ts of primers and probes compared to a large sequence database such as nt.

248 ch services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and mo

249 e over 200 homologs of similar size in large sequence databases such as UniProt, with pairwise sequen

250 PRO complements established sequence databases such as UniProtKB, and interoperates

251 , we identified a bacteriophytochrome in the sequence database that is monomeric in truncated form an

252 e protein matching, however, have such large sequence databases that the resulting list of seeds cann

253 iously unreported gene (not present in human sequence databases) that encodes an inwardly rectifying

254 show that as more sequences are added to the sequence databases the fraction of sequences that Pfam m

255 n to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology

256 n to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology

257 tion to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology

258 n to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology

259 tion to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology

260 tion to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology

261 many sources, including the EMBL Nucleotide Sequence Database, the UniProt Knowledgebase, InterPro,

262 ty, and those involved in development of HCV sequence databases, the Hepatitis Virus Database (Japan)

263 s because of the lack of appropriate protein sequences databases, thus restricting the analysis on co

264 es a search mode using a query STS against a sequence database to augment the previously available mo

265 equences against the U12-type spliced intron sequence database to examine whether some events could o

266 cognition), we constructed a three-locus DNA sequence database to facilitate molecular identification

267 beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes

268 We use the largest publicly available exome sequence database to show that this key clinical service

269 nterface allows a range of different protein sequence databases to be searched including the SCOP dat

270 To test this concept, we searched public sequence databases to identify putative LHE open reading

271 pportunities for laboratories to parse large sequencing databases to identify proteins and noncoding

272 ced by searching the spectra against a decoy sequence database, to provide a model of the null score

273 Using the nr-sequence database together with a reference protein set

274 We present three clustered protein sequence databases, Uniclust90, Uniclust50, Uniclust30 a

275 The sequence database used to calculate sequence profiles wa

276 ood ratio score for each position in a given sequence database, uses established dynamic programming

277 hat pass all filters are then located in the sequence database using a precomputed index, and an accu

278 e searched against an appropriate nucleotide sequence database using tools such as BLAST to examine t

279 We searched the Drosophila protein sequences database using fully characterized insect chit

280 ion) of gene and protein function over large sequence databases, using phylogenetic trees to extrapol

281 ms that can be used to search many different sequence databases via the BLAST web pages.

282 os Alamos National Laboratory Oral Pathogens Sequence Database was identified, which was strongly ind

283 The HCV sequence database was officially launched in September 2

284 -length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist

285 Using extensive sequence databases, we compared the characteristics of n

286 Using public and proprietary sequence databases, we discovered one novel human PTP ge

287 ive BLAST searches of public and proprietary sequence databases, we further identified orthologous se

288 vantage of the ongoing exponential growth of sequence databases, we go significantly beyond anecdotal

289 Unlike other public DNA sequence databases, we include multiple indigenous popul

290 od and semen samples from the Los Alamos HIV Sequence Database were analyzed to ascertain a male geni

291 The patterns found in a protein sequence database were used to create decoy databases us

292 ound changes in the taxonomic composition of sequence databases, which are effectively redefining the

293 report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotide

294 pe-phenotype relations from population-based sequence databases, which is an integral facet of person

295 log with known 3D structure when searching a sequence database with an arbitrary query sequence.

296 d, we conducted a BLASTN search of the maize sequence database with queries from two previously descr

297 proximately equal to 200 bp) against a large sequence database with small memory footprint (e.g. ~2 G

298 rpreted product ion spectrum against protein sequence databases with varying degrees of annotation, c

299 of de novo and spectra matching to a protein sequence database, with up to 4077 peptides (2725 modifi

300 atch, is able to cross-link any of the major sequence databases within a few seconds on a modest desk