ライフサイエンスコーパス: microbial genome

1 -scale sRNA identification for any sequenced microbial genome.

2 ning the number and sizes of ORFs within any microbial genome.

3 rediction of functional modules encoded in a microbial genome.

4 set of microbial contigs against a completed microbial genome.

5 striction sites at any given nucleotide in a microbial genome.

6 ical virulence strategies encoded within the microbial genome.

7 ts per liter that mapped to several thousand microbial genomes.

8 y from the perspective of both our human and microbial genomes.

9 es of interest from metagenomes and complete microbial genomes.

10 the human reference genome to a database of microbial genomes.

11 discovery within archaeal and other selected microbial genomes.

12 l in several studies of completely sequenced microbial genomes.

13 econdary metabolites are a common feature of microbial genomes.

14 SIV R1-R2 fusion are found in many sequenced microbial genomes.

15 the discovery of cryptic peptides encoded in microbial genomes.

16 footprint of positive Darwinian selection in microbial genomes.

17 epertoire of signal transduction proteins in microbial genomes.

18 d for improving the annotations of about 150 microbial genomes.

19 algorithm for locating operon structures in microbial genomes.

20 m genome scale metabolic models derived from microbial genomes.

21 ilable addressing its occurrence in complete microbial genomes.

22 ependent approach to sample and characterize microbial genomes.

23 netic distribution of rRNA and tRNA genes in microbial genomes.

24 OGs] database) are encoded by many plant and microbial genomes.

25 d annotating sequence data, particularly for microbial genomes.

26 highly reproducible and quality analysis of microbial genomes.

27 tronic catalog of the signaling machinery in microbial genomes.

28 the average content of previously sequenced microbial genomes.

29 sent an algorithm for pathway mapping across microbial genomes.

30 prediction of functional modules encoded in microbial genomes.

31 ormed a comparative analysis of 72 sequenced microbial genomes.

32 omated high-throughput mutation detection in microbial genomes.

33 gies conserved (without disablements) across microbial genomes.

34 s between all orthologous proteins within 44 microbial genomes.

35 tree consisting of 3,240 publicly available microbial genomes.

36 putative genes found by sequence analysis of microbial genomes.

37 organization between finished and unfinished microbial genomes.

38 nucleotide combinations in 27 representative microbial genomes.

39 verage protein length comparisons for all 44 microbial genomes.

40 or determining the near-complete sequence of microbial genomes.

41 and can be adapted for the investigation of microbial genomes.

42 ine is proposed to find potential operons in microbial genomes.

43 density high-throughput analyses of complete microbial genomes.

44 y to be biologically relevant in 17 complete microbial genomes.

45 ring algorithm for protein-coding regions in microbial genomes.

46 a new system, GLIMMER, for finding genes in microbial genomes.

47 esis will require analyses of populations of microbial genomes.

48 Such sequences are not common in microbial genomes.

49 red biological activities that are hidden in microbial genomes.

50 ation about the unique k-mers present in the microbial genomes.

51 nd systematic functional characterization of microbial genomes.

52 ed to achieve saturating coverage of complex microbial genomes.

53 om sequence locus typer tool for classifying microbial genomes.

54 but is impeded by the mosaic organization of microbial genomes.

55 G DNA motifs that are most commonly found in microbial genomes.

56 ing selective isolation of DNA segments from microbial genomes.

57 alibrating the markers using data from known microbial genomes.

58 strate the value of mining viral signal from microbial genomes.

59 ged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body si

60 Using 5390 sequenced microbial genomes, 8 770 321 50-mer strain-specific and

61 In addition, new information describing microbial genomes affords the opportunity to mine for fu

62 ies, they can generate de novo assemblies of microbial genomes, after an initial correction step that

63 ether with new technologies for manipulating microbial genomes, allowed such questions to be addresse

64 availability of a large number of sequenced microbial genomes allows us to conduct systematic studie

65 ER) and teaching and training in the area of microbial genome analysis (IMG/EDU).

66 nnotations, teaching courses and training in microbial genome analysis and analysis of genomes relate

67 Although microbial genome analysis indicates that photoactive B(1

68 It is designed to automate the main steps in microbial genome analysis-assembly, gene prediction, fun

69 ons and teaching and training in the area of microbial genome analysis.

70 whole genome shotgun sequencing approach for microbial genome analysis.

71 sequencing that have driven the explosion of microbial genome and community profiling projects, and t

72 Microbial genome and metagenome application specific dat

73 etagenome datasets are processed using IMG's microbial genome and metagenome sequence data processing

74 ) contains robust annotation of all complete microbial genomes and allows for a wide variety of data

75 ntiSMASH results for many publicly available microbial genomes and allows for advanced cross-genome s

76 widely distributed in ~10% of all sequenced microbial genomes and can be divided into six coherent s

77 iocin encoding genes are frequently found in microbial genomes and could therefore offer a ready supp

78 The increasing availability of microbial genomes and environmental shotgun metagenomes

79 locus tags from 1835 OA publications in ten microbial genomes and extracted tags mentioned in 30,891

80 We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS

81 The lack of microbial genomes and isolates from the deep seabed mean

82 The integrated microbial genomes and metagenomes (IMG/M) system provide

83 Scientists studying microbial genomes and metagenomes often need one or seve

84 aking advantage of the expanding database of microbial genomes and metagenomes, combined with direct

85 e offers phylogenetic analysis of genes from microbial genomes and metagenomes.

86 entified 10,295 inovirus-like sequences from microbial genomes and metagenomes.

87 ate that Canu can reliably assemble complete microbial genomes and near-complete eukaryotic chromosom

88 R-cas loci are widely distributed throughout microbial genomes and often display hallmarks of horizon

89 nine (6mA) modification is commonly found in microbial genomes and plays important functions in regul

90 The increase in full microbial genomes and similar resources has led to devel

91 es has enabled precise, multiplex editing of microbial genomes and the construction of billions of cu

92 sion medicine that encompasses our human and microbial genomes and their combined metabolic activitie

93 ynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query

94 mologous recombination and point mutation in microbial genomes, and present evidence for two distinct

95 g agents, explains the well-known GC skew in microbial genomes, and suggests the APOBEC3 family of mu

96 To do so, we augmented the MAGPIE microbial genome annotation system to handle eukaryotic

97 ends of genes is of critical importance for microbial genome annotation, especially in light of the

98 It also is important for current efforts in microbial genome annotation.

99 porting systematic and efficient revision of microbial genome annotations.

100 Seventeen microbial genomes archived at ftp://ncbi.nlm.nih.gov/gen

101 Detailed restriction maps of microbial genomes are a valuable resource in genome sequ

102 In this technology, hundreds of entire microbial genomes are arrayed, rather than sequences of

103 Microbial genomes are available at an ever-increasing pa

104 New microbial genomes are constantly being sequenced, and it

105 Microbial genomes are covered by IMG/M and resources for

106 logeny has demonstrated that the majority of microbial genomes are currently inaccessible.

107 though the complete DNA sequences of several microbial genomes are now available, nearly 40% of the p

108 Several thousand microbial genomes are now available, necessitating new a

109 A rapidly increasing number of microbial genomes are sequenced by organizations worldwi

110 While hundreds of microbial genomes are sequenced, the challenge remains t

111 ing technologies have brought recognition of microbial genomes as a rich resource for novel natural p

112 llows selective isolation of any region from microbial genomes as well as from environmental DNA samp

113 surveyed data banks of completely sequenced microbial genomes, as well as those for genomes in the p

114 During the year of 2014 more than 10,000 microbial genome assemblies have been publicly released

115 A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without

116 mbly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-in

117 sertions/deletions are thought to be rare in microbial genome assemblies, fourteen of the loci contai

118 Microbial genomes at the National Center for Biotechnolo

119 y verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (I

120 her metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a ge

121 Quantification and identification of microbial genomes based on next-generation sequencing da

122 With many more microbial genomes being sequenced, such a strategy could

123 t links for each gene to UCSC eukaryotic and microbial genome browsers provide graphical display of t

124 SMRT) sequencing is routinely used to finish microbial genomes, but available assembly methods have n

125 r trillions of bases can uncover hundreds of microbial genomes, but naive assembly of these data is c

126 Microbial genomes can be assembled from short-read seque

127 In this way, microbial genomes can evolve to become ecologically dive

128 Microbial genomes can now be sequenced in a matter of ho

129 Differences in microbial genomes can result in vastly different phenoty

130 apid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analy

131 n stages, and represent different degrees of microbial genome characterization.

132 conservation of genetic information between microbial genomes, combined with the exponential increas

133 rate higher-quality lower-cost assemblies of microbial genomes compared to current Sanger sequencing

134 e analysis of the ever-growing collection of microbial genomes coupled with experimental validation e

135 Vastly greater quantities of microbial genome data are being generated where environm

136 er to derive maximum knowledge from existing microbial genome data as well as from genome sequences t

137 e last years, the increasing availability of microbial genome data has made it possible to access the

138 ta resources manage the results of different microbial genome data processing and interpretation stag

139 issive profile alignments based on available microbial genome data.

140 Examination of the Integrated Microbial Genomes database revealed that orthologs of th

141 agenomic sequencing allows reconstruction of microbial genomes directly from environmental samples.

142 trial microbial commodities, and patterns of microbial genome diversity.

143 summary, results of this study indicate that microbial genomes do indeed contain detectable signal of

144 ng step in adaptive laboratory evolution and microbial genome engineering.

145 dence previously uncharacterized LGT (~2 per microbial genome-equivalent).

146 Here, we report a quantitative analysis of microbial genome evolution by fitting the parameters of

147 to a generalized framework for understanding microbial genome evolution in a spatial context.

148 e trees to be related to broader patterns in microbial genome evolution is scant, and therefore micro

149 Microbial genome evolution is shaped by a variety of sel

150 ng gene content and sequence across multiple microbial genomes facilitating the discovery of genetic

151 was explored by conducting a BLAST search of microbial genomes followed by phylogenetic analysis.

152 Projects designed to scan entire microbial genomes for essential genes have revealed a re

153 To explore the value added by choosing microbial genomes for sequencing on the basis of their e

154 se pairs of metagenomic sequences and 24 903 microbial genomes for tRNA(Sec) species.

155 il ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one

156 nt a systematic evaluation using 42 complete microbial genomes from 25 phylogenetic groups to test th

157 vides a unique tool to understand pathogenic microbial genomes from a global perspective.

158 A) provides an efficient approach to amplify microbial genomes from complex backgrounds for sequence

159 omparisons with a control group representing microbial genomes from diverse natural environments indi

160 ing approach for high-throughput recovery of microbial genomes from metagenomes.

161 ence of single-copy marker genes to separate microbial genomes from non-model host genomes and other

162 We find that 23% of microbial genomes from premature infant guts have sidero

163 tating the de novo assembly of near-complete microbial genomes from single Escherichia coli cells.

164 integrates metagenome data sets with isolate microbial genomes from the IMG system.

165 s of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes

166 We thus identify thousands of microbial genomes from yet-to-be-named species, expand t

167 s (10.2x depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 yea

168 Microbial genomes harbor an abundance of biosynthetic ge

169 Although microbial genomes harbor an abundance of biosynthetic ge

170 rs of functionally related genes in multiple microbial genomes has enormous potential for enhancing s

171 Sequencing of a large number of microbial genomes has led to the discovery of new enzyme

172 The availability of complete microbial genomes has made genome-wide TU predictions po

173 The availability of microbial genomes has opened many new avenues of researc

174 The complete sequencing of several microbial genomes has resulted in the increased availabi

175 Recent molecular characterization of various microbial genomes has revealed differences in genome siz

176 Increased sequencing of microbial genomes has revealed that prevailing prokaryot

177 otein products identified in fully sequenced microbial genomes have been compared with proteins with

178 An increasing number of microbial genomes have been completely sequenced, and th

179 Thousands of candidate BGCs from microbial genomes have been identified and stored in pub

180 At present, hundreds of microbial genomes have been sequenced, and hundreds more

181 be about 250,000 protein families when 1000 microbial genomes have been sequenced.

182 Around two dozen microbial genomes have now been completed and, within a

183 Analyses of sequenced microbial genomes have revealed an enormous number of bi

184 C. difficile clade, or indeed, in any other microbial genome; however, smaller segments were detecte

185 The Integrated Microbial Genomes (IMG) data warehouse integrates genome

186 des a seamless interface with the Integrated Microbial Genomes (IMG) system and supports and promotes

187 e depositing sequence data to the Integrated Microbial Genomes (IMG) system for analysis.

188 Launched in March 2005, the Integrated Microbial Genomes (IMG) system is a comprehensive data m

189 The integrated microbial genomes (IMG) system is a data management, ana

190 The integrated microbial genomes (IMG) system is a new data management

191 The Integrated Microbial Genomes (IMG) system serves as a community res

192 The integrated microbial genomes (IMG) system serves as a community res

193 Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of support

194 solate microbial genomes from the Integrated Microbial Genomes (IMG) system.

195 lysis system that is based on the Integrated Microbial Genomes (IMG) system.

196 Compiling such information across microbial genomes improves the functional classification

197 The detailed database for every microbial genome in NCBI is commercially available throu

198 tunities for investigation of AMR across all microbial genomes in a sample (i.e. the metagenome).

199 Metagenomics studies microbial genomes in an ecosystem such as the gastrointe

200 As DNA can be introduced into microbial genomes in many ways, the compact nature of th

201 we investigate the resistome of 435 ruminal microbial genomes in silico and confirm representative p

202 s are widespread in numerous uncharacterized microbial genomes, in which an ORF17 homolog is always a

203 quence DNA samples isolated from a number of microbial genomes including 750-kb Ureaplasma urealyticu

204 protein disulfide bonds for over one hundred microbial genomes, including both bacterial and achaeal

205 e sequence data from an ever-growing list of microbial genomes, including complete genomes for multip

206 The core properties of microbial genomes, including GC content and genome size,

207 es improve and the number of whole sequenced microbial genomes increases, a user-friendly genome cont

208 Examination of approximately 1,000 sequenced microbial genomes indicated that such biosynthetic pathw

209 The availability of microbial genome information has provided a fruitful opp

210 IMG contains both draft and complete JGI microbial genomes integrated with all other publicly ava

211 IMG contains both draft and complete microbial genomes integrated with other publicly availab

212 microbial species has demonstrated that the microbial genome is a dynamic entity shaped by multiple

213 Mapping biological pathways across microbial genomes is a highly important technique in fun

214 s and the complete sequencing of a number of microbial genomes is providing the opportunity to compre

215 Analysis of public microbial genomes leads to the discovery of over sixty t

216 The sequence of microbial genomes made all potential antigens of each pa

217 rizontal gene transfer is well documented in microbial genomes, no case has been reported in higher p

218 mes integrated with other publicly available microbial genomes of all three domains of life.

219 tive method for predicting relatedness among microbial genomes of B. cereus group members and potenti

220 Thus, new genes acquired by microbial genomes, on average, appear to be adaptive.

221 cAB orthologues are rare among all available microbial genomes, organisms are much more phylogenetica

222 rcular contigs from sequence data of isolate microbial genomes, plasmidome and metagenome sequence da

223 single species level by considering the 106 microbial genomes previously identified.

224 f the complete prokaryotic genomes in NCBI's Microbial Genome Project Database and applying statistic

225 d on the controlled vocabularies that NCBI's Microbial Genome Project database uses to specify the or

226 ys) of uncharacterized enzymes discovered in microbial genome projects using the ligand specificities

227 ew data management and analysis platform for microbial genomes provided by the Joint Genome Institute

228 netic transfer in shaping the composition of microbial genomes, providing novel metabolic capabilitie

229 on information deriving from the sequence of microbial genomes rather than via the growth of pathogen

230 mapped specifically to intergenic regions of microbial genomes recovered from similar habitats, displ

231 Here we investigate thousands of viral and microbial genomes recovered using a cultivation-independ

232 However, finding prophages in microbial genomes remains a problem with no definitive s

233 ologous genes (COGs) from 44 fully sequenced microbial genomes representing all three domains of life

234 to improve the quality and usability of the microbial genome resources by providing easy access to t

235 and integration with RegTransBase and other microbial genome resources.

236 Mrr superfamily of homologous genes in microbial genomes restricts modified DNA in vivo.

237 Analysis of the approximately 631 kb microbial genome revealed strong evidence of an endosymb

238 Current analysis of available microbial genomes reveals that "eukaryote-like" protein

239 ated DNAs (microsatellites) in nine complete microbial genomes (Saccharomyces cerevisiae, Archaeoglob

240 Since the publication of the first complete microbial genome sequence of Haemophilus influenzae in 1

241 It is the smallest microbial genome sequenced to date, and also one of the

242 oximately one-third of all genes) across all microbial genomes sequenced to date, have homologs in mo

243 r interpreting the large number of reference microbial genome sequences being generated for the Inter

244 n DNA sequencing technologies, the number of microbial genome sequences has increased dramatically, r

245 omparative analysis of the growing number of microbial genome sequences has shown a high plasticity o

246 influenzae in 1995, more than 200 additional microbial genome sequences have become available in the

247 The growing number of complete microbial genome sequences provides a powerful tool for

248 s, coupled with the availability of complete microbial genome sequences, provide insight almost as fa

249 We demonstrate that errors in microbial genome sequences, thought to largely be confin

250 database system designed to host a range of microbial genome sequences.

251 Recent microbial genome sequencing efforts have uncovered many

252 Microbial genome sequencing has revealed a plethora of u

253 Microbial genome sequencing in particular has evolved fr

254 Microbial genome sequencing is driven by the need to und

255 Microbial genome sequencing is one of the longest-standi

256 Microbial genome sequencing projects are beginning to pr

257 However, as more microbial genome sequencing projects are completed, it i

258 Microbial genome sequencing projects produce numerous se

259 s are often sufficient to fill final gaps in microbial genome sequencing projects without additional

260 Microbial genome sequencing thus represents not a threat

261 comprehensive resource under the torrent of microbial genome sequencing.

262 less obscure, due in part to large-scale gut microbial genome-sequencing projects and culture-indepen

263 Marine metagenomes and microbial genomes show that Verrucomicrobia including 'L

264 vidence for the inverse relationship between microbial genome size and temperature in a diverse, free

265 nymous to synonymous substitution rates, and microbial genome size.

266 e largest number characterized in functional microbial genomes so far.

267 ve organism to study how environment impacts microbial genome structure and function.

268 epeats (CRISPR) were detected in most of the microbial genomes, suggesting previous interactions betw

269 he method to a newly sequenced and annotated microbial genome, Synechococcus sp. WH8102, through a co

270 However, microbial genomes that are currently available are of li

271 ional) lists of close homologs from complete microbial genomes that are more likely to crystallize.

272 e approach the completed sequencing of 1,000 microbial genomes, the field of microbial genomics is po

273 zae , Helicobacter pylori and other complete microbial genomes, this system has proven to be very acc

274 We applied this algorithm to 42 microbial genomes to identify putative operon structures

275 ns ranging from the assembly of uncultivable microbial genomes to the identification of cancer-associ

276 uding the use of fragment libraries of whole microbial genomes, to identify peptide-ligand and protei

277 e-scale datasets containing information from microbial genomes together with antimicrobial susceptibi

278 Since the first microbial genome was sequenced in 1995, 30 others have b

279 For each of 30 completely sequenced microbial genomes, we established all such fusion links

280 To facilitate SNP discovery in microbial genomes, we have developed a web-based applica

281 Although several microbial genomes were recently sequenced, the described

282 ondition that is violated for most sequenced microbial genomes where BGCs are often scattered through

283 argely based on (i) its reliance on complete microbial genomes, which allowed reliable assignment of

284 ine and chemokine receptor homologs found in microbial genomes, which deflect the immune response of

285 ific markers (GSMs) from currently sequenced microbial genomes, which were then used for strain/speci

286 We also assembled 15 uncultured microbial genomes, which were validated by complementary

287 PATRIC and MicroScope update in microbial genomes while human and model organism genomic

288 istically rigorous approach to extract novel microbial genomes while preserving single-cell resolutio

289 t (i) can determine the overall quality of a microbial genome, while providing a putative phylogeneti

290 microorganisms, enabling the application of microbial genome-wide association studies (GWAS).

291 We additionally use a microbial genome-wide-association study (GWAS) approach

292 The release of the 1000th complete microbial genome will occur in the next two to three yea

293 The Integrated Microbial Genomes with Microbiome Samples system contain

294 For microbial genomes with very few functionally characteriz

295 D subsystems technology, first developed for microbial genomes, with refined protein families and bio

296 notations of both new and publicly available microbial genomes within IMG's rich integrated genome fr

297 ol microbiome samples generated over 150 000 microbial genomes without any culture, vastly expanding

298 ncRNAs in partially or completely sequenced microbial genomes without requiring homology or structur

299 erited genetic entities and aids assembly of microbial genomes without the need for reference sequenc

300 ematically, the presence of recombination in microbial genomes would go undetected unless other genom