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

8 footprint of positive Darwinian selection in microbial genomes.

9 epertoire of signal transduction proteins in microbial genomes.

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

11 algorithm for locating operon structures in microbial genomes.

12 om sequence locus typer tool for classifying microbial genomes.

13 ilable addressing its occurrence in complete microbial genomes.

14 ependent approach to sample and characterize microbial genomes.

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

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

17 d annotating sequence data, particularly for microbial genomes.

18 tronic catalog of the signaling machinery in microbial genomes.

19 the average content of previously sequenced microbial genomes.

20 sent an algorithm for pathway mapping across microbial genomes.

21 prediction of functional modules encoded in microbial genomes.

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

23 ormed a comparative analysis of 72 sequenced microbial genomes.

24 omated high-throughput mutation detection in microbial genomes.

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

26 gies conserved (without disablements) across microbial genomes.

27 s between all orthologous proteins within 44 microbial genomes.

28 putative genes found by sequence analysis of microbial genomes.

29 organization between finished and unfinished microbial genomes.

30 nucleotide combinations in 27 representative microbial genomes.

31 verage protein length comparisons for all 44 microbial genomes.

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

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

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

35 density high-throughput analyses of complete microbial genomes.

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

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

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

39 ed to achieve saturating coverage of complex microbial genomes.

40 alibrating the markers using data from known microbial genomes.

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

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

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

44 es of interest from metagenomes and complete microbial genomes.

45 discovery within archaeal and other selected microbial genomes.

46 l in several studies of completely sequenced microbial genomes.

47 econdary metabolites are a common feature of microbial genomes.

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

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

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

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

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

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

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

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

56 whole genome shotgun sequencing approach for microbial genome analysis.

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

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

59 Microbial genome and metagenome application specific dat

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

78 porting systematic and efficient revision of microbial genome annotations.

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

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

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

82 horizontal gene transfer predictions for 123 microbial genomes are available online at http://cbcsrv.

83 New microbial genomes are constantly being sequenced, and it

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

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

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

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

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

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

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

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

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

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

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

95 Microbial genomes at the National Center for Biotechnolo

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

111 issive profile alignments based on available microbial genome data.

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

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

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

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

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

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

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

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

120 Microbial genome evolution is shaped by a variety of sel

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

140 Increased sequencing of microbial genomes has revealed that prevailing prokaryot

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

156 Compiling such information across microbial genomes improves the functional classification

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

179 e result of the transcriptome analysis for a microbial genome Porphyromonas gingivalis W83 can be vie

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

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

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

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

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

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

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

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

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

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

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

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

192 and integration with RegTransBase and other microbial genome resources.

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

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

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

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

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

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

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

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

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

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

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

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

205 DarkHorse algorithm has been applied to 955 microbial genome sequences, and the results organized in

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

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

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

209 Microbial genome sequencing in particular has evolved fr

210 Microbial genome sequencing is driven by the need to und

211 Microbial genome sequencing is one of the longest-standi

212 Microbial genome sequencing projects are beginning to pr

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

214 Microbial genome sequencing projects produce numerous se

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

216 Microbial genome sequencing thus represents not a threat

217 comprehensive resource under the torrent of microbial genome sequencing.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

234 Although several microbial genomes were recently sequenced, the described

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

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

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

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

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

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

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

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

243 The Integrated Microbial Genomes with Microbiome Samples system contain

244 For microbial genomes with very few functionally characteriz

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

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

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

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

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