ライフサイエンスコーパス: genome annotation

1 ertain drawbacks with regards to prokaryotic genome annotation.

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

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

4 metry data as a complementary technology for genome annotation.

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

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

7 ity was consistent with predictions from the genome annotation.

8 tively spliced isoforms, contrary to current genome annotation.

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

10 ion of duplicate genes and benefiting future genome annotation.

11 will play an increasingly important role in genome annotation.

12 gene structures, thus improving the existing genome annotation.

13 and policies regarding species inclusion and genome annotation.

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

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

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

17 g functional sequence categories and improve genome annotation.

18 rs to contribute directly toward the ongoing genome annotation.

19 ranscription units that will facilitate rice genome annotation.

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

21 hod for obtaining an experimentally verified genome annotation.

22 enes in many eukaryotes and a key element in genome annotation.

23 -that of the rat--suggests a need to rethink genome annotation.

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

25 xplore intraspecies sequence comparisons for genome annotation.

26 rotein function and evolution as well as for genome annotation.

27 ical networks, and the GESTALT workbench for genome annotation.

28 ne set and demonstrate its utility for plant genome annotation.

29 be a highly efficient method for functional genome annotation.

30 are identified, making the method useful for genome annotation.

31 y, implying utility for automated eukaryotic genome annotation.

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

33 databases, and predicted enzyme location and genome annotation.

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

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

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

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

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

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 web-based applications to visualize various genome annotations.

48 factors with context information taken from genome annotations.

49 applications is the improvement of existing genome annotations.

50 ly hosted Internet-accessible collections of genome annotations.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

65 comprehensive web-based system for community genome annotation and analysis.

66 ttern discovery, automated domain detection, genome annotation and ancestral reconstruction.Conclusio

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

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

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

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

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

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

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

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

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

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

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

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

79 proach has broad potential use as a tool for genome annotation and for the characterization of global

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

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

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

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

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

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

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

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

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

89 H. pylori strain 26695 based on the revised genome annotation and new experimental data.

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

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

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

93 osed of repetitive sequences that can hinder genome annotation and sequencing efforts.

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

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

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

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

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

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

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

101 Genome annotations and biochemical studies indicate that

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

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

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

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

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

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

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

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

110 examined the updated (20.02.02) Riley group genome annotation, and examined the scientific literatur

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

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

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

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

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

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

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

118 Curation of the E. chrysanthemi genome annotation as well as those of additional publish

119 ST databases provide essential resources for genome annotation as well as transcriptome characterizat

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

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

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

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

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

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

126 profiles, trained from a database of curated genome annotations, can be used to reliably detect error

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

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

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

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

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

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

133 croarray platforms based on diverse types of genome annotation data (across different species) collec

134 an be integrated and overlaid with extensive genome annotation data using GALA.

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

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

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

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

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

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

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

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

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

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

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

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

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

151 well as being one of the leading sources of genome annotation, Ensembl is an open source software en

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

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

154 A whole genome annotation for nucleosome exclusion regions (NXRe

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

156 Thus, genome annotation for retrogene identification should di

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

158 Genome annotations for all sequenced strains of Dehaloco

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

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

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

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

163 he probe set sequences were derived from the genome annotation generated by Oak Ridge National Labora

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

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

166 Many model organism databases and genome annotation groups use the GO and contribute their

167 Prokaryotic genome annotation has been focused mainly on identifying

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

169 While bacterial genome annotations have significantly improved in recent

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

171 gh it is not obvious from examination of the genome annotation how these bacteria utilize methionine.

172 Genome annotation identified 27,263 protein-coding gene

173 scanning method has the potential to aid in genome annotation, identify proteins for which annotatio

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 Genome annotation in differently evolved organisms prese

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

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

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

182 ew the relationships among the corresponding genome annotations in detail.

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

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

185 Given that genome annotation is a largely predictive process, key c

186 Genome annotation is a synthesis of computational predic

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

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

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

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

191 A promising strategy for refining genome annotations is to detect features that conflict w

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

193 Through genome annotation many features of interest were identif

194 We conclude that genome annotation may entail a considerable amount of er

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

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

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

198 Significant challenges remain in genome annotation methods, including the identification

199 sequences overlooked by previous Arabidopsis genome annotation methods.

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

201 In genome annotation, multiple methods are often run and ag

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

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

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

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

206 ased on a systematic literature curation and genome annotation of DNase I footprints for the fruitfly

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 The original genome annotation of the hyperthermophilic archaeon Pyro

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

211 ce to reference sequences in addition to the genome annotations of the focus sequence.

212 The web site also links to whole genome annotations of the human, mouse and rat genomes p

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

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

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

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

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

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

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

220 set of sources, including those typical of a genome annotation pipeline.

221 have been incorporated into the Prokaryotic Genome Annotation Pipeline.

222 Genome annotation pipelines collect a variety of types o

223 tor identification has been largely based on genome annotation pipelines that use pairwise sequence c

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

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

226 Functional genome annotation predicts that at least 66 potential PM

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

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

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

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

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

232 ASD data has been integrated with Ensembl genome annotation project as a Distributed Annotation Sy

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

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

235 Genome annotation projects have generally become small-s

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

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

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

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

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

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

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

243 Full genome annotation requires gene expression analysis and

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

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

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 This emphasizes that genome annotation should take into account the fact that

250 comparison with other genomics data such as genome annotation, SNPs, or gene expression, there exist

251 fication of orthologous groups is useful for genome annotation, studies on gene/protein evolution, co

252 Genome annotation suggested that early-diverged kinetopl

253 ultiple members of a species can be used for genome annotation, suggesting a path for the annotation

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

255 While genome annotation suggests the absence of most tricarbox

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

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

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

263 f quantitative trait analysis for functional genome annotation through forward genetics.

264 e Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0).

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

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

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

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

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

270 To assess the current state of mouse genome annotation to support this activity, we identifie

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

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

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

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

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

276 Genome annotations typically include assembly data, sequ

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

278 The Vertebrate Genome Annotation (Vega) database has been designed to b

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

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

281 database is currently used by the Vertebrate Genome Annotation (VEGA) site, which provides access to

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

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

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

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

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

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

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

289 Numerous improvements to T. maritima genome annotations were proposed, including the identifi

290 The new genome annotations were stored in VIOLIN, an interactive

291 inating true coding regions are critical for genome annotation when other sources of evidence for fun

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

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

294 This updated Arabidopsis genome annotation with a substantially increased resolut

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

296 database provides a tool for high-throughput genome annotation with maximal specificity and sensitivi

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.