ライフサイエンスコーパス: GenBank

1 quences that is used to check submissions to GenBank.

2 the common files required for submission to GenBank.

3 390 full-length human HCV 1a sequences from GenBank.

4 lar to any genes with annotated functions in GenBank.

5 y annotation namespaces, e.g. KEGG or NCBI's GenBank.

6 ing for the deposition of 4,850 sequences to GenBank.

7 uated by testing from 27 to 240 genomes from GenBank.

8 capsid sequence from 56 strains available in GenBank.

9 up of randomly selected Ig heavy chains from Genbank.

10 ions were stable across successive builds of GenBank.

11 cs sites and community data archives such as GenBank.

12 the cloned fragments with the nr-database in Genbank.

13 t GenBank table files prior to submission to GenBank.

14 nces were identified, 3 of which were not in GenBank.

15 he 11 complete genome sequences available in GenBank.

16 g maize DNA sequences currently available in GenBank.

17 ster virus have been published and listed in GenBank.

18 l databases, such as EntrezGene, UniProt and GenBank.

19 at the protein level with other sequences in GenBank.

20 isms with sequenced genome, available in the GenBank.

21 (UniProt) and the associated mRNA data from Genbank.

22 otein that has no apparent homologues within GenBank.

23 454 technology, but that lacked orthologs in GenBank.

24 quences from genetic databases, particularly GenBank.

25 facilitate virus genome submissions to NCBI GenBank.

26 691 high-quality H. influenzae genomes from GenBank.

27 inst authenticate published ITS sequences in GenBank.

28 ifies itself and nothing else in a search of GenBank.

29 en the compared RH1 sequences and those from GenBank.

30 All known sequences were extracted from GenBank.

31 um, and its sequences have been deposited in GenBank.

32 were carried out with sequences deposited in GenBank.

33 a clonal activating point mutation in HRAS (GenBank 3265) (c.37G-->C) in the Spitz nevi and underlyi

34 The apolipoprotein E (APOE [GenBank, 348; OMIM, 107741]) epsilon4 allele is a common

35 One of these lncRNAs, SPRY4-IT1 (GenBank accession ID AK024556), is derived from an intro

36 ce of novel allele, named as OsPLDalpha1-1a (GenBank accession no.

37 RNA gene sequencing as Segniliparus rugosus (GenBank accession no. AY 60892).

38 Streptomyces sp. PB-79 (GenBank accession no. KU901725; 1313 bp), Streptomyces s

39 Streptomyces sp. Kz-24 (GenBank accession no. KY000533; 1367 bp) showed only 96.

40 KU901725; 1313 bp), Streptomyces sp. Kz-28 (GenBank accession no. KY000534; 1378 bp), Streptomyces s

41 KY000534; 1378 bp), Streptomyces sp. Kz-32 (GenBank accession no. KY000536; 1377 bp) and Streptomyce

42 000536; 1377 bp) and Streptomyces sp. Kz-67 (GenBank accession no. KY000540; 1383 bp) showed ~89.5% s

43 nes encoding COMT, designated Mdomt1-Mdomt5 (GenBank accession nos.

44 as an environmental stress-responsive gene (GenBank accession number AL049644.1, locus spcc191.01).

45 novel human PKCdelta isozyme, PKCdeltaVIII (Genbank accession number DQ516383) in human teratocarcin

46 GenBank accession number for Danio rerio disc1: EU273350

47 K14-vGPCR/ORF74 mRNA, terminating at 130873 (GenBank accession number GQ994935), resulting in an appr

48 herin 15 CD3 pointed to amino acids 158-179 (GenBank accession number XP_238200), with homology to th

49 ctional risk variant, named BV677278 for its GenBank accession number, for RD in DCDC2.

50 ers for the gene(s) of interest, such as by: GenBank accession number, NCBI protein accession number,

51 Supplementary data, including GenBank Accession numbers, are available at Bioinformati

52 are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic ancho

53 ther identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnecte

54 were annotated, of which 19,786 have unique GenBank accession numbers.

55 GenBank accession numbers: DISC1FP1 (EU302123), Boymaw (

56 GenBank Accession Numbers: FJ010164-FJ010174.

57 GenBank Accession Numbers: GQ850461-GQ850464.

58 GenBank accession numbers: KF041446, KF041447, KF041448,

59 GenBank accession, Number: MK333199-333226.

60 Their sequences were deposited in GenBank [accession numbers GQ465348 to GQ465370].

61 rature, online reports, strain archives, and GenBank accessions.

62 romosome 19p13 to which NTE had been mapped (GenBank AJ004832).

63 ed by the yeast Yarrowia lipolytica (YLLIP2; GenBank: AJ012632) might be used in PERT.

64 of a Lingulodinium EST dataset deposited in GenBank and 94% of the enzymes in 16 primary metabolic K

65 he species and sequences present in the NCBI GenBank and allows for a single step classification of m

66 an 400 ITS1- and ITS2-related sequences from GenBank and an in-depth evaluation of the length variati

67 or batch submissions of different viruses to GenBank and correctly annotates multiple viruses, includ

68 ific community, prediction, propagation from GenBank and curation by NCBI staff.

69 atabases, and remote sequence retrieval from GenBank and dbSNP.

70 orted at this position in all mammals in the GenBank and Ensembl databases, with arginine reported in

71 Based on the sequences published in GenBank and Ensembl, we designed specific primers and de

72 plished by querying public databases such as GenBank and examining the geospatial metadata in the rec

73 development of central repositories such as GenBank and Gene Expression Omnibus.

74 Unlike other NCBI databases, such as GenBank and Gene, which have a strict data structure, bo

75 l that we use to flag sequences from type in GenBank and in Genomes.

76 ysis and retrieval resources for the data in GenBank and other biological data available through NCBI

77 ysis and retrieval resources for the data in GenBank and other biological data made available through

78 ysis and retrieval resources for the data in GenBank and other biological data made available through

79 ysis and retrieval resources for the data in GenBank and other biological data made available through

80 ysis and retrieval resources for the data in GenBank and other biological data made available through

81 AST provides sequence similarity searches of GenBank and other sequence databases.

82 p up with the continuous flow of new data in GenBank and RefSeq.

83 quences reported in this study) available in GenBank and reported from 23 countries were characterize

84 s of those managing public databases such as GenBank and SwissProt.

85 agenomic search by extracting sequences from GenBank and the 1000 Genomes Project.

86 aking advantage of the exponential growth of GenBank and the creation of NCBI's RefSeq database, we h

87 because of the large number of sequences in GenBank and the large number of highly similar paralogue

88 0 complete bacterial genomes and plasmids in GenBank and were capable of detecting 82% of the ISs and

89 pared to all complete sequences available in GenBank, and haplotype analysis demonstrated 92 haplotyp

90 114,035, and 14,148 sequences in the RefSeq, GenBank, and NR databases, respectively, spanning the wh

91 tent with the corresponding information from GenBank, and produced better performance compared to exi

92 and improves the content and quality of the GenBank annotations.

93 ization specifications via Python scripts or Genbank annotations.

94 on, 3615 genome sequences occupying 56 MB in GenBank are compressed down to only 167 KB, achieving a

95 EST sequence accession numbers in GenBank are EH 795234 through EH 995233 and EL 000001 th

96 We show that metazoan identifications in GenBank are surprisingly accurate, even at low taxonomic

97 id not resemble any known phage sequences in GenBank as of August 2006.

98 34 420 nifH sequences were identified in GenBank as of November 20, 2012.

99 seen R and the Gene Ontology join BLAST and GenBank as the main components in bioinformatics process

100 rresponding to a gene currently annotated in Genbank as TSGA2 homolog (mouse) to signify 'testis spec

101 0% of cDNA and mRNA sequences contributed to GenBank before the patent application was filed also con

102 Bear Paw; a finding consistent with those of Genbank BLAST.

103 corrected sample dates modified by others in GenBank but also corrected an additional transcriptional

104 omes currently in LINbase were imported from GenBank, but users can upload their own genome sequences

105 ced and compared with sequences available in GenBank by phylogenetic analysis.

106 hic Alu insertions in sequences submitted to GenBank by screening the elements against reference geno

107 that can be used for sequence submission to GenBank (by Sequin or tbl2asn), a GenBank flat file, or

108 peed with which non-flu virus submissions to GenBank can be checked and improves the content and qual

109 of the software allow researchers to run the GenBank checks prior to submitting their viral sequences

110 n this study combined with 339 obtained from GenBank), collected from patients in 36 provinces in Vie

111 lenok Brachymystax tumensis and analyzed the GenBank complete mt genomes of related species.

112 lly annotate over 2500 complete genomes in a GenBank-compliant format.

113 <30% of the prokaryotic genomes submitted to GenBank contain partial repeat features of specific type

114 GenBank contains over 3 million viral sequences.

115 GenBank currently has automatic prokaryotic and eukaryot

116 arly in the context of missing or incomplete GenBank data, and, whenever possible, should be evaluate

117 ted in this paper have been deposited in the GenBank database (accession nos.

118 ces of the circulating HIV-1 isolates in the GenBank database and observed that, in addition to the p

119 bi-monthly releases and daily updates of the GenBank database are available by FTP.

120 bimonthly releases and daily updates of the GenBank database are available by FTP.

121 More than 97% of HBV BCP sequences in the GenBank database can be correctly identified by the melt

122 ional Center for Biotechnology Information's GenBank database is problematic because of annotation er

123 a strain of M. catarrhalis available in the GenBank database was analyzed, and open reading frames p

124 6S rRNA gene, listed as G. ferruginea in the GenBank database.

125 quences of Aspergillus spp. deposited in the GenBank database.

126 their homology to annotated sequences in the GenBank database.

127 ted in this paper have been deposited in the GenBank database.

128 ose of other ascaridomorphs available in the GenBank database.

129 einhardtii expressed sequence tags (ESTs) in GenBank dbEST and community EST assemblies were either o

130 tweight command-line tool for annotation and GenBank deposition of viral genomes.

131 Few GenBank deposits were found to be complete for either re

132 ore, legacy bioinformatics file formats like GenBank do not provide enough information about the purp

133 e data from this article can be found in the GenBank/EMBL data libraries under accession numbers BE 6

134 e data from this article can be found in the GenBank/EMBL data libraries under accession numbers DU 6

135 from this study have been submitted to DDBJ/GenBank/EMBL under accession numbers EU940701-EU977132 (

136 Swiss-Prot, in turn, relies on GenBank/Embl/DDJP for predicted proteins from complete g

137 tabase Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases.

138 f which 108 exhibited high similarities with Genbank entries.

139 E products for antisense transcripts and the GenBank EST database revealed that TART antisense transc

140 26 samples (including sequences available at GenBank) examined by the developed assays and a recently

141 European Molecular Biology Laboratory (EMBL)/GenBank feature table format for reading and displaying

142 In addition to the DDBJ/EMBL/GenBank feature table format, we share metadata formats

143 encing, and produce an annotated sequence in Genbank file format as output.

144 It combines gene annotations from GenBank files and other sources with information retriev

145 hat can take any combination of fasta files, GenBank files and/or NCBI assembly accessions as input a

146 hical user interface, validation of uploaded GenBank files, and abilities to import phages from exist

147 pri-miR-199a2 within the human Dnm3os gene (GenBank FJ623959).

148 gene annotation and DNA sequence data from a GenBank flat file, (ii) displaying patterns of gene cons

149 mission to GenBank (by Sequin or tbl2asn), a GenBank flat file, or the predicted protein sequences in

150 r groups that do not routinely interact with GenBank for data submissions.

151 tional Center of Biotechnology Information's GenBank for downstream analysis including phylogeography

152 The number of draft genomes deposited in Genbank from the National Center for Biotechnology Infor

153 ssORF to compare gene predictions offered by GenBank, GeneMarkS-2, Glimmer and Prodigal on genomes sp

154 the MG1655 Genbank record, one of only a few Genbank genome records that are updated by a community e

155 gy Information, comprises a set of duplicate Genbank genome records that can be modified by the NCBI

156 erlapping 400 to 900-bp records found in the Genbank Genome Survey Sequence database.

157 OS reference genomes compared to non-curated GenBank genomes.

158 NREF, PIR, Gene Ontology, KEGG, Entrez Gene, GenBank, GenPept, IMAGE, RefSeq, UniGene, OMIM, PDB, Euk

159 y method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases,

160 divergent regions are identical between the GenBank H. taimen and two lenok subspecies, B. lenok and

161 A comparison of the data with the GenBank H. taimen mt genome (HQ897271) reveals significa

162 1.89 to 8.68, were further confirmed in 163 GenBank HBV-HCC sequences from nine Asia regions, assaye

163 proportions of sequences without significant Genbank homology, which has hampered identification of v

164 This was confirmed by analysis of the GenBank Human EST database, which revealed the presence

165 demonstrating that the gene encoding Q5LIW1 (GenBank ID YP_209877.1) was able to complement an API-de

166 novirus to be sequenced and was deposited in GenBank in 1999.

167 ly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships

168 tomatically, without the need for any human (GenBank indexer) intervention.

169 GenBank is a comprehensive database that contains public

170 GenBank is a comprehensive database that contains public

171 GenBank is a comprehensive database that contains public

172 Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays

173 GenBank is accessible through NCBI's retrieval system, E

174 GenBank is accessible through the National Center for Bi

175 GenBank is accessible through the NCBI Entrez retrieval

176 GenBank is accessible through the NCBI Entrez retrieval

177 GenBank is accessible through the NCBI Nucleotide databa

178 GenBank is accessible through the nuccore, nucest, and n

179 Sequences from GenBank, isolated from diseased plants between 1988 and

180 c reference for resources such as PubMed and GenBank, it has grown to its current size of >1300 title

181 ntative set of known structures and searches GenBank iteratively.

182 as been paid to the taxonomic reliability of GenBank itself.

183 his particular four-amino acid region, GPPT (GenBank KC329849) versus DLQL (GenBank NC004293), respec

184 The gene (GenBank # KU304333.1) consists of a single exon, encodin

185 These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene

186 heuristic utilizing knowledge obtained from GenBank metadata (i.e. a 'metadata heuristic').

187 sets such as the nucleotide database in NCBI GenBank, metagenomic datasets in Camera, and the marine

188 nce from annotations of UCSC Known Genes and GenBank mRNA.

189 vel promoters we looked into other evidences-GenBank mRNAs, spliced ESTs, CAGE promoter tags and mRNA

190 taN, proposed from bioinformatic analysis of GenBank (National Center for Biotechnology Information,

191 region, GPPT (GenBank KC329849) versus DLQL (GenBank NC004293), respectively at residues 389-392.

192 omenclature based on the longest transcript (GenBank: NM_001128227), which encodes a 31-amino acid lo

193 ion c.722dupA (p.Val242Glyfs( *)33) in PEX5 (GenBank: NM_001131023.1).

194 nonymous variants were identified in IQSEC1 (GenBank: NM_001134382.3).

195 .Arg1173Leu), and c.3008G>A, (p.Gly1003Asp) (GenBank: NM_001273.3), affect evolutionarily highly cons

196 fied a homozygous splice donor site variant (GenBank: NM_001378.2:c.607+1G>A).

197 identified two homozygous variants in SPARC (GenBank: NM_003118.3; c.497G>A [p.Arg166His] in individu

198 r protein than the originally described one (GenBank: NM_005476), which has been used previously in m

199 osyl-oligosaccharide glucosidase) mutations (GenBank: NM_006302.2; c.[65C>A; 329G>A] p.[Ala22Glu; Arg

200 a recurrent CNOT1 de novo missense mutation, GenBank: NM_016284.4; c.1603C>T (p.Arg535Cys), resulting

201 ividuals had a homozygous c.692dup mutation (GenBank: NM_022167.3) in the xylosyltransferase II locus

202 r example, the HNF4A c.340C>T (p.Arg114Trp) (GenBank: NM_175914.4) variant associated with diabetes i

203 In addition to maintaining the GenBank nucleic acid sequence database, the National Cen

204 In addition to maintaining the GenBank nucleic acid sequence database, the National Cen

205 expressed sequences collected from the NCBI GenBank Nucleotide database for the construction of tran

206 This motif has no homologs in GenBank or PROSITE and is unique to flightin and parafli

207 GenBank organizes the sequence data received from indivi

208 f the genome sequences were misidentified in GenBank, our virulence results were used to inform our b

209 ving all genomic DNA sequences from the NCBI GenBank, over 1 x 10(11) base pairs of 3.3 x 10(6) seque

210 iales are probably divergent bicoeceans (the GenBank Placidia sequence is a basidiomycete/heterokont

211 f the participating databases, DDBJ, ENA and GenBank, principles of data exchange within the collabor

212 utative environmental peritrich sequences at Genbank, produced a comprehensive tree of peritrichs fro

213 selected taxonomic group have accumulated in GenBank, PUmPER automatically extends the alignment and

214 GenBank (R) is a comprehensive database that contains pu

215 GenBank (R) is a comprehensive database that contains pu

216 GenBank(R) is a comprehensive database that contains pub

217 GenBank(R) is a comprehensive database that contains pub

218 GenBank(R) is a comprehensive database that contains pub

219 ological information and data, including the GenBank(R) nucleic acid sequence database and the PubMed

220 In addition to maintaining the GenBank(R) nucleic acid sequence database, the National

221 In addition to maintaining the GenBank(R) nucleic acid sequence database, the National

222 In addition to maintaining the GenBank(R) nucleic acid sequence database, the National

223 grams, and accession numbers are assigned by GenBank(R) staff upon receipt.

224 GenBank((R)) is a comprehensive database that contains p

225 ry three-marker analysis including taxa from GenBank raises this number to 107 species from 48 genera

226 + links each pseudoknot in PseudoBase to the GenBank record of the corresponding nucleotide sequence

227 source of annotation updates for the MG1655 Genbank record, one of only a few Genbank genome records

228 ana barcode sequences (n = 247, including 24 GenBank records) formed a monophyletic lineage separate

229 he only published IL-10 sequence existing in Genbank reported from C4D guinea pigs, genomic DNA was i

230 shows that it maps to 22q13 rather than the GenBank reported locus of 22p13.

231 notyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS N

232 lysis of these genomes and 1011 genomes from GenBank revealed a distinct cluster, confirming a new Eb

233 Searching the database of GenBank revealed that a large number of expressed sequen

234 1 CGs (30 CGs from our study and 48 CGs from GenBank) revealed two HPV11 lineages (lineages A and B)

235 T similarity (E-value <10-5) to sequences in GenBank's non-redundant databases, indicating that a lar

236 We searched for these extra genes in both GenBank's non-redundant protein database and all of the

237 t, only approximately 9000 are catalogued in GenBank's RefSeq database.

238 nclature variation and paralogues; moreover, GenBank's structure and tools are not conducive to searc

239 VADR has been integrated into GenBank's submission processing pipeline allowing for vi

240 arity to published sequences in unrestricted GenBank searches, and there are no significant open read

241 .4 strains identified in this study and from GenBank segregated these viruses into at least 9 distinc

242 ational Center for Biotechnology Information Genbank sequence data archive.

243 ragments between the donor and the recipient GenBank sequence suggests that the introgression is loca

244 This sequence, along with other GenBank sequences from past EV-D68 occurrences, was used

245 A BlastP search of GenBank sequences revealed five glutamine amidotransfera

246 graphers that rely on geospatial metadata of GenBank sequences.

247 ded sequences and the sequences deposited in GenBank showed plausible misidentifications, and the use

248 ples, and other mammalian cells available in GenBank showed the predominance of a specific structure

249 ed BankIt or standalone Sequin programs, and GenBank staff assign accession numbers upon data receipt

250 GenBank staff assign accession numbers upon data receipt

251 e sequencing projects into 18 divisions, and GenBank staff assign unique accession.version identifier

252 ed BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receip

253 Reciprocally, the adoption of VADR frees GenBank staff to spend more time on services other than

254 grams, and accession numbers are assigned by GenBank staff upon receipt.

255 ograms and accession numbers are assigned by GenBank staff upon receipt.

256 ediately without the need to correspond with GenBank staff.

257 Before GenBank submission, EST sequences are typically screened

258 The gene feature table can be used to create GenBank submission.

259 Most GenBank submissions are made using BankIt, the NCBI Subm

260 sequences were mined from EST databases and GenBank submissions from four insect orders: Coleoptera

261 We reviewed all GenBank submissions of HIV-1 reverse transcriptase seque

262 ew version of Genome Workbench that supports GenBank submissions, new submission wizards for viral ge

263 t validates and annotates viral sequences in GenBank submissions.

264 gnificant homology with proteins reported in GenBank, suggesting that the genus Emaravirus evolved fu

265 logenies built from 2.6 million sequences in GenBank suggests that signal is strong in vertebrates an

266 similarity to known protein sequences within GenBank, Syn5 shares features with T7-like phages.

267 The PNU can also be used to correct GenBank table files prior to submission to GenBank.

268 In Genbank the protein deduced from this gene is currently

269 n to displaying the original annotation from GenBank, the CMR makes available secondary automated str

270 Data are publicly available from GenBank, the HapMap web site, and the MITOMAP database.

271 ious name for nitronate monooxygenase in the GenBank(TM) and PDB databases, but the enzyme was not ki

272 similarity 4,985 genes are annotated in the GenBank(TM) as NMO.

273 n more than 490 hypothetical proteins in the GenBank(TM), the vast majority of which are currently mi

274 s and validated complete coding sequences in GenBank to (1) regroup the individual probes into consis

275 c survey of all lasso peptides identified in GenBank to perform coevolutionary analysis of two requis

276 s full genomes of influenza A available from Genbank to provide an auto-updating documentation of the

277 e alignment tool that generates contigs from GenBank trace file data and BioExtract Server, a web-bas

278 Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI.

279 lyze the metazoan mitochondrial sequences of GenBank using a combination of distance-based clustering

280 A sequence comparison search of GenBank using BLASTP revealed several full-length paralo

281 ng a set of 2133 complete phage genomes from GenBank, using PHANOTATE and the three most popular gene

282 IncHI2 plasmids carrying mcr-1 available in GenBank was performed based on core genes.

283 genomes associated with known outbreaks from GenBank, we constructed a maximum-likelihood phylogeneti

284 eptides from other Conus species recorded in GenBank, we date the major duplication events after the

285 with the non-redundant set of corn mRNAs in GenBank, we estimate that there are about 50,000 differe

286 risons with available DNA sequence data from GenBank, we estimate the number of species-level genetic

287 of Staphylininae from published DNA data in GenBank, we generated a well-resolved phylogeny of Staph

288 By mining DNA microarray data bases at GenBank, we identified up-regulation of membrane type 1

289 th 332 Chinese HRSVB sequences obtained from GenBank were analyzed to determine the geographic and ye

290 clusters for which the first blastn hits in GenBank were members of the known bee phylotypes.

291 ther with 766 HRSV sequences downloaded from GenBank, were analyzed to understand the recent circulat

292 e a novel gene, OSTL (annotated as RNF217 in Genbank), which shares the first exon and a CpG island w

293 reviously existing R. reniformis sequence in GenBank, while the RN_VAR2 sequence is more divergent.

294 82% of the ISs and transposases annotated in GenBank with 80% sequence identity.

295 rRNA gene clone sequences were deposited in GenBank with Accession No. JQ366086-JQ387568.

296 ctuca (SsHV2L) and deposited the sequence in GenBank with accession number KF898354.

297 n this work we utilized A-B PCR and screened GenBank with sequences from isolated clones to identify

298 om putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a dire

299 hers currently submit annotated sequences to GenBank without significant external taxonomic validatio

300 ical sequence formats, including UniProtXML, Genbank XML, FASTA and FASTQ.