ライフサイエンスコーパス: genome annotation

1 view and browse test statistics and perform genome annotation.

2 ent of protein-coding genes is a key goal of genome annotation.

3 r for prokaryotes and is a valuable tool for genome annotation.

4 l can be obtained directly from an automated genome annotation.

5 rocess appears to be absent from the current genome annotation.

6 ertain drawbacks with regards to prokaryotic genome annotation.

7 nd MNase-seq have become important tools for genome annotation.

8 RF genes, 56 were new to the current Populus genome annotation.

9 metry data as a complementary technology for genome annotation.

10 tional analyses to critical tasks like phage genome annotation.

11 rons that are not represented in the current genome annotation.

12 and that it can improve transcriptome-based genome annotation.

13 ity was consistent with predictions from the genome annotation.

14 tively spliced isoforms, contrary to current genome annotation.

15 rate a highly aggregated report of the human-genome annotation.

16 ion of duplicate genes and benefiting future genome annotation.

17 will play an increasingly important role in genome annotation.

18 These findings can refine Arabidopsis genome annotation.

19 gene structures, thus improving the existing genome annotation.

20 and policies regarding species inclusion and genome annotation.

21 cellular reactions, 27) that were not in the genome annotation.

22 needed for growth but were not found in the genome annotation.

23 rent analyses, such as sequence analysis and genome annotation.

24 g functional sequence categories and improve genome annotation.

25 rs to contribute directly toward the ongoing genome annotation.

26 ranscription units that will facilitate rice genome annotation.

27 the identification of DNA-binding sites and genome annotation.

28 lar targets but also be an essential role in genome annotation.

29 he most challenging problems in the field of genome annotation.

30 al short comings including a low coverage in genome annotation.

31 RMs) is an important goal of post-sequencing genome annotation.

32 Gene is a key step in genome annotation.

33 data sets and can be used for collaborative genome annotation.

34 genomic loci to receive the same label in a genome annotation.

35 databases, and predicted enzyme location and genome annotation.

36 oCanyon a unique and powerful tool for whole-genome annotation.

37 ly hosted Internet-accessible collections of genome annotations.

38 patterns, and both pre-installed and custom genome annotations.

39 ic regions of arbitrary length without using genome annotations.

40 genomic regions as well as the accompanying genome annotations.

41 tivity and enhanced the accuracy of existing genome annotations.

42 stematic and efficient revision of microbial genome annotations.

43 ain specific needs, such as expert review of genome annotations.

44 most accurate, complete and multidimensional genome annotations.

45 al subsystems to provide the most consistent genome annotations.

46 genes encoding peptides are often missed in genome annotations.

47 the sufficiency and completeness of natural genome annotations.

48 nd ab initio prediction to generate accurate genome annotations.

49 n or relying on the availability of existing genome annotations.

50 applications is the improvement of existing genome annotations.

51 atics is to make these genomic sequences and genome annotations accessible in a user-friendly manner

52 orest model was applied to several automated genome annotations, achieving an accuracy of ~60% in mos

53 s created to provide consistent and accurate genome annotations across thousands of genomes and as a

54 me alignments synchronized with a display of genome annotations along each axis.

55 Using the rice (Oryza sativa) sp. japonica genome annotation, along with genomic sequence and clust

56 automatic data-mining algorithms to keep the genome annotation always up-to-date; (iii) comparative g

57 project exploits and extends technology (for genome annotation, analysis and dissemination) developed

58 roject exploits and extends technologies for genome annotation, analysis and dissemination, developed

59 The Ensembl project is a system for genome annotation, analysis, storage and dissemination d

60 n metabolic network based on Build 35 of the genome annotation and a comprehensive evaluation of >50

61 better understanding of the relation between genome annotation and actual metabolic pathways in D. vu

62 Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere

63 ere mostly likely missed in the current rice genome annotation and another 500 genes for structural a

64 on of poly(A) tails is essential to improved genome annotation and better understanding of the regula

65 A sequences is an important and open task in genome annotation and bioinformatics.

66 been used for data management in a number of genome annotation and comparative genomics projects.

67 creating, maintaining and updating reference genome annotation and comparative genomics resources.

68 s from all kingdoms, which allows systematic genome annotation and comparative insights for CYPs.

69 upport bovine genomics research by providing genome annotation and data mining tools.

70 for the combined assembly, gene prediction, genome annotation and data presentation necessary to int

71 ectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P

72 profiling has emerged as a powerful means of genome annotation and detection of regulatory activity.

73 New transcripts, missing in the current TIGR genome annotation and ESTs that are non-coding, includin

74 have become increasingly necessary for both genome annotation and evolutionary studies.

75 is a powerful tool for transcript discovery, genome annotation and expression profiling.

76 By grouping SNPs based on genome annotation and fitting multiple random effects, w

77 nscription factor binding site searches with genome annotation and gene expression profiling data, to

78 method should prove a useful tool in aiding genome annotation and gene expression studies in both pr

79 By bringing together M. tuberculosis genome annotation and gene-expression data with a suite

80 mon bioinformatics tasks such as prokaryotic genome annotation and genome comparisons.

81 key metabolites clarifies ambiguities in the genome annotation and identifies an unusual biosynthetic

82 suggest that RNA-Seq significantly improves genome annotation and identifies novel genes and isoform

83 us to add 365 genes that were missed during genome annotation and identify 917 gene correction event

84 set covers 87% of the current S. cerevisiae genome annotation and includes full sequencing of each O

85 Consistent with the current genome annotation and independent evidence from enzyme a

86 Knowledge of Psis can improve genome annotation and our understanding of genome evolut

87 y detection algorithms are valuable tools in genome annotation and protein classification.

88 Es can also greatly simplify many downstream genome annotation and sequence analysis tasks.

89 internet-enabled, open-source, command-line genome annotation and submission package to facilitate v

90 xins is expanding through advances in cereal genome annotation and terpene synthase characterization

91 Supported by the genome annotation and the transcript profile, isotopomer

92 , automatic pipelines can produce inaccurate genome annotation and their results often require manual

93 ntinues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest

94 fflux pump gene (CBU1362) were identified by genome annotation and using a Fur titration assay.

95 ntific interest, developed using the Ensembl genome annotation and visualisation platform.

96 his new release features updates to previous genome annotations and a substantial number of newly ava

97 Genome annotations and biochemical studies indicate that

98 researchers can confirm and revise existing genome annotations and discover completely new genes.

99 the original effort to connect each model to genome annotations and external databases as well as sta

100 BiGG Models connects genome-scale models to genome annotations and external databases.

101 different ways and compare the results with genome annotations and other genome scans.

102 viewing the data in the context of reference genome annotations and other related datasets.

103 publicly available genomes, expert review of genome annotations and teaching and training in the area

104 tudies of these data have relied on existing genome annotations and thus are limited to the analysis

105 ol for undergraduate students to learn about genome annotation, and a means for the community of rese

106 uences provide a valuable resource for maize genome annotation, and are a uniquely valuable complemen

107 e accurate determination of gene structures, genome annotation, and exploration of the transcriptome

108 proteins is one of the biggest challenges of genome annotation, and perhaps more importantly, few ann

109 ate Research Experiences (CUREs) centered on genome annotation, and students to participate in genomi

110 rovides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and

111 gly on their local genomic context, accurate genome annotations are essential.

112 ntity between strain pairs is 98%, and their genome annotations are similar.

113 For example, when genome annotations are updated or new understanding rega

114 the Companion web server providing parasite genome annotation as a service using a reference-based a

115 nalysis, drug design, disease diagnosis, and genome annotation as a vast number of protein sequences

116 eful to the Tribolium research community for genome annotation as well as comparative genomics.

117 The nematode genome annotation assessment project (nGASP) was launche

118 systematic assessment of the accuracy of the genome annotation based on a detailed analysis of a comp

119 s is an integral and significant part of the genome annotation because of their abundance and their i

120 such as whole-genome shotgun sequencing and genome annotation by a community "jamboree," the Drosoph

121 it chromatin conformation information during genome annotation by encouraging positions that are clos

122 complementary DNA (cDNA) sequencing can aid genome annotation by revealing transcript structure and

123 ODE project has improved the D. melanogaster genome annotation by using deep and diverse high-through

124 To augment the BGD genome annotation capabilities, we have developed a new

125 uence and residue coverage can be useful for genome annotation, comparative genomics and functional s

126 RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical te

127 s provide songbird biologists with tools for genome annotation, comparative genomics, and microarray

128 m Buchnera sp. APS that includes an improved genome annotation, comparative information about related

129 ical knowledge, it is readily applicable for genome annotation comparison and genome re-annotation pr

130 quickest and most feature-rich solution for genome annotation comparison to date.

131 ryophyta dataset suggested that, on average, genome annotation completeness was 85.6%.

132 al domain-specific annotation data alongside genome annotation data from multiple repositories.

133 Despite increased availability of genome annotation data, a comprehensive resource for in-

134 We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structur

135 X:Map is a genome annotation database that provides this informatio

136 ncing 737 genes (annotated in the Vertebrate Genome Annotation database) on the human X chromosome in

137 rieve genome annotation features from a UCSC genome annotation database, display histograms of non-re

138 Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to

139 mation system featuring an integrated set of genome annotation, databases and other information for c

140 mation system featuring an integrated set of genome annotation, databases, and other information for

141 nalysed in different ways and projected onto genome annotations derived from EnsMart.

142 to facilitate community efforts in improving genome annotation, determining accurate gene structures

143 However, due to incomplete genome annotations, draft metabolic models contain gaps

144 opy number alterations, gene expression, and genome annotations (e.g. gene and regulatory elements) t

145 ariation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar,

146 ytical approach that incorporates functional genome annotations (e.g., exon or 5'UTR), total linkage

147 Apollo is a genome annotation-editing tool with an easy to use graph

148 tensive analyses and Apollo, a collaborative genome annotation editor, visualizes the results of thes

149 ould be revised as part of the ongoing human genome annotation effort.

150 ngine MAKER in order to better support plant genome annotation efforts.

151 Thus, the present method of genome annotation employed at this early pandemic stage

152 ve developed MAKER-P, a fast and easy-to-use genome annotation engine for plants.

153 to correct such inconsistencies during whole-genome annotation, equivalent software designed to corre

154 cally generated reference sequence, retrieve genome annotation features from a UCSC genome annotation

155 oot of this problem is the use of incomplete genome annotation files.

156 A whole genome annotation for nucleosome exclusion regions (NXRe

157 This approach will assist genome annotation for paleopolyploid and true polyploid

158 Thus, genome annotation for retrogene identification should di

159 y generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegan

160 Genome annotations for all sequenced strains of Dehaloco

161 ource to integrate SVs, gene expression, and genome annotations for discovering biologically relevant

162 A comparison to genome annotations for other model organisms shows that

163 nd assembly-based pipelines in all available genome annotations from the Brassicaceae, including mult

164 multidrug-resistant S. aureus strains using genome annotation, functional-pathway analysis, and comp

165 s serve as a valuable community resource for genome annotation, gene dynamics and comparative functio

166 rowing RBP experimental data with the latest genome annotation, gene function, RNA sequence and struc

167 the integration of computational and manual genome annotations generated by NCBI, Ensembl and Vega/H

168 terpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems bi

169 Prokaryotic genome annotation has been focused mainly on identifying

170 The rice genome annotation has been greatly improved in recent ye

171 While bacterial genome annotations have significantly improved in recent

172 The parallel view displays two genome annotations horizontally, synchronized through a

173 Genome annotation identified 27,263 protein-coding gene

174 alysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a

175 Tasks like genome annotation, image analysis, knowledge-base popula

176 available genomes (IMG/W), expert review of genome annotations (IMG/ER) and teaching and training in

177 Although the genome annotation implicates a ferredoxin-dependent oxog

178 n-based strategies can be used for improving genome annotation in other microorganisms, especially th

179 cing purposes, as well as efforts to improve genome annotation in the fragmented assemblies produced

180 rver, WebGBrowse that allows users to upload genome annotation in the GFF3 format, configure the disp

181 rafish, taking advantage of the high-quality genome annotation in this species.

182 ce into an Apollo instance for collaborative genome annotations in research and educational settings.

183 ed the entire database to reflect changes to genome annotations, included information on cyclin-depen

184 learned decision structure is shared across genome annotations including histone marks, DNase hypers

185 Genome annotation is a continuing effort, and many of th

186 Genome annotation is a synthesis of computational predic

187 Genome annotation is an important step for all in-depth

188 ch can be applied to any organism as long as genome annotation is available.

189 ation, a comprehensive approach to automatic genome annotation is critically needed.

190 to understanding gene function, and accurate genome annotation is essential for understanding cellula

191 At the CPT, genome annotation is separated into two robust segments

192 Genome annotation is the process of identifying the loca

193 The integration of genome annotations is critical to the identification of

194 to less well-characterized cell types during genome annotation, making it possible to produce high-qu

195 Through genome annotation many features of interest were identif

196 ide insights into when and how computational genome annotations may benefit future complex disease st

197 ted SHARKhunt tool or from other programs or genome annotations, may be uploaded to the website and o

198 atory elements is essential for high-quality genome annotation, metabolic reconstruction, and modelin

199 Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised stat

200 Semi-automated genome annotation methods such as Segway take as input a

201 sequences overlooked by previous Arabidopsis genome annotation methods.

202 ddition, we found that a number of reference genome annotations might need to be updated due to the h

203 s of the names of individual proteins in the genome annotation of an organism.

204 analysis significantly enhances the current genome annotation of C. albicans, a necessary framework

205 ective method for transcriptome analysis and genome annotation of complex genomes.

206 esearch communities will greatly improve the genome annotation of different protein families in publi

207 tion and propose improvements to the current genome annotation of F. prausnitzii A2-165.

208 for FLu ANnotation), the NCBI web server for genome annotation of influenza virus is a tool for user-

209 , has been proposed and successfully used in genome annotations of eukaryotes.

210 e present the full structural and functional genome annotations of six Juglans species and one outgro

211 functions including read cataloging based on genome annotation, optional seed region check, miRNA fam

212 owser, JBrowse, that can be used to navigate genome annotations over the web.

213 ments in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy

214 Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequenc

215 developed a portable and easily configurable genome annotation pipeline called MAKER.

216 Recent changes to NCBI's eukaryotic genome annotation pipeline provide higher throughput, an

217 mbly, RefSeq, viral genomes, the prokaryotic genome annotation pipeline, Genome Workbench, dbSNP, BLA

218 nges and using the programs within the MAKER genome annotation pipeline, we were able to improve the

219 have been incorporated into the Prokaryotic Genome Annotation Pipeline.

220 tly has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation

221 Genome annotation pipelines collect a variety of types o

222 ing genes are frequently overlooked, because genome annotation pipelines generally ignore small open

223 atic training has become paramount, allowing genome annotation pipelines to keep pace with the speed

224 Biotechnology Information (NCBI) and Ensembl genome annotation pipelines.

225 Functional genome annotation predicts that at least 66 potential PM

226 fy common problems introduced by the current genome annotation process and suggests potential solutio

227 Here we provide an overview of the genome annotation process and the available tools and de

228 asic requirement in the initial steps of any genome annotation process.

229 cate several thousand gene models during the genome annotation process.

230 on is one of the most important steps in the genome annotation process.

231 In The Institute for Genomic Research Rice Genome Annotation project, we have continued to update t

232 m from our participation in the GO Reference Genome Annotation Project--a multi-database collaboratio

233 Genome annotation projects have generally become small-s

234 nomics datasets and to perform collaborative genome annotation projects in both research and educatio

235 e has had a significant impact on eukaryotic genome annotation, providing protein kinase annotations

236 warehousing system, to integrate the bovine genome, annotation, QTL, SNP and expression data with ex

237 to a variety of use cases including de novo genome annotation, reannotation, comparison of different

238 aunch of several TAIR web services and a new genome annotation release (TAIR7) in April 2007.

239 mapping, de novo assembly or visualization, genome annotation remains a challenge.

240 mplete eukaryotic genomes are available, and genome annotation remains a major challenge.

241 d and their potential for systematic de novo genome annotation remains untapped.

242 Full genome annotation requires gene expression analysis and

243 ond with 50 attributes from 17 commonly used genome annotation resources.

244 Semi-automated genome annotation (SAGA) algorithms facilitate human int

245 ne boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophistic

246 We have developed a web-based prokaryotic genome annotation server, Integrative Services for Genom

247 Different genome annotation services have been developed in recent

248 s that improvements of the current P. yoelii genome annotation should focus on genes expressed in sta

249 Yaravirus genome annotation showed that none of its genes matched

250 d assembly of many thousands of new genomes, genome annotation still uses very nearly the same techno

251 k these two features, we introduce IMPACT, a genome annotation strategy that identifies regulatory el

252 Genome annotation suggested that early-diverged kinetopl

253 d biosynthesis pathways, even though current genome annotation suggests that several of these pathway

254 While genome annotation suggests the absence of most tricarbox

255 PSAT stands apart from other sequence-based genome annotation systems in providing a high-throughput

256 rk and include virus origin, genome quality, genome annotation, taxonomic classification, biogeograph

257 systems provide support for expert review of genome annotations, teaching courses and training in mic

258 a Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods

259 1, a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMa

260 Here we describe an automated pipeline for genome annotation that integrates RNA-seq and gene-bound

261 g comparative transcriptomic data to improve genome annotation that is fundamental for connecting gen

262 DNA methylation represents a form of genome annotation that mediates gene repression by servi

263 epend on the quality and completeness of the genome annotation, there are substantial efforts in the

264 Although not noted in the original genome annotation, TM0504 was found to colocate, on the

265 hese findings have implications ranging from genome annotation to de novo assemblies and could enable

266 onsortium to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58

267 applied to broad research areas ranging from genome annotation to proteomics data analysis.

268 ized miRNAs as training samples, and rely on genome annotation to reduce the number of predicted puta

269 ce genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome feat

270 The EnzymeDetector genome annotation tool and the reaction database BKM-rea

271 yme classification, motif identification and genome annotation tool using a bipartite network algorit

272 entation of RepeatMasker, we developed a new genome annotation tool, DupMasker.

273 deler2 represents a valuable addition to the genome annotation toolkit that will enhance the identifi

274 Existing genome annotation tools focus on annotating intact genes

275 This GBT system facilitates novel functional genome annotation towards understanding cellular and mol

276 It also produces genome annotation tracks of the biomedical literature, t

277 sequencing data) with both public and custom genome annotation tracks.

278 Genome annotations typically include assembly data, sequ

279 sualizing a large number of file formats for genome annotation, variant calling, reads coverage and g

280 th different frequencies; and the quality of genome annotation varies greatly.

281 The number of RGAs, based on genome annotations, varies within and between species.

282 The Vertebrate Genome Annotation (Vega) database was first made public

283 The Vertebrate Genome Annotation (VEGA) database, initially designed as

284 annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline.

285 at may not be directly inferable solely from genome annotation was developed.

286 The genome annotation was performed using the RAST service.

287 L. tarentolae and L. major genome annotation was transferred and these gene models

288 To facilitate precision medicine and whole-genome annotation, we developed a machine-learning techn

289 ur CRE-seq results to a comprehensive set of genome annotations, we identified a variety of genomic f

290 To improve genome annotations, we linearly integrate these sequence

291 The predicted SRPN9 and 15 in the initial genome annotation were determined to be a single gene (S

292 Several reactions not predicted by the genome annotation were postulated and validated via the

293 In addition, we provide an interface for genome annotation, which like all of the tools reported

294 Additionally we updated the entire genome annotation with 113 new features including previo

295 This updated Arabidopsis genome annotation with a substantially increased resolut

296 demonstrate the importance of complementing genome annotation with isotope tracer studies for determ

297 genes from tRNA genes is a tricky problem in genome annotation without assumptions on length of DNA a

298 ate the automated generation of high-quality genome annotations without the need for extensive manual

299 gy for discovery of sORFs in species with no genome annotation yet available.

300 tron/exon boundaries is an essential part of genome annotation, yet remains a challenge.