ライフサイエンスコーパス: EMBL

1 f the European Molecular Biology Laboratory (EMBL).

2 vailable in public databases (SWISS-PROT and EMBL).

3 f the European Molecular Biology Laboratory (EMBL).

4 f the European Molecular Biology Laboratory (EMBL).

5 f the European Molecular Biology Laboratory (EMBL).

6 xternal data sources (e.g. NCBI taxonomy and EMBL).

7 atabase is available at http://www.ebi.ac.uk/embl/.

8 We report 5805bp of novel sequence (GenBank/EMBL Accession No.

9 A fourth variant reported earlier (GenBank/EMBL accession No.

10 anum tuberosum), designated POTLX-3 (GenBank/EMBL accession no. U60202), in defense responses against

11 ells expressing the rat heart RHE-1 (NCX1.1, EMBL accession number ) or the rat brain RBE-2 (NCX1.5,

12 encing project has identified a gene (orf16, EMBL accession number D38161) which exhibits significant

13 The alignments are stored in the EMBL-Align database and can be queried from the EBI SRS

14 in CLUSTALW format as well as a new standard EMBL-Align flat file format.

15 abase of multiple sequence alignments called EMBL-Align.

16 ww.ebi.ac.uk/embl/Submission/align_top.html, EMBL-Align: ftp://ftp.ebi.ac.uk/pub/databases/embl/align

17 MBL-Align: ftp://ftp.ebi.ac.uk/pub/databases/embl/align, http://srs.ebi.ac.uk/

18 ration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases.

19 Nucleotide Sequence Database (www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK,

20 These include extended EMBL-Bank and SRA-data submission services, extended ENA

21 search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed geno

22 EMBL-Bank is located and maintained at the European Bioi

23 t patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protei

24 , the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Univer

25 s, which store information on DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), p

26 , APIs exist for core data resources such as EMBL-Bank, Ensembl, UniProt, InterPro, PDB and ArrayExpr

27 ce Read Archive (SRA), the Trace Archive and EMBL-Bank.

28 Information on the EMBL CORBA servers is at http://corba.ebi.ac.uk/

29 syntax, there is now a demand to distribute EMBL data in an XML format.

30 rom this article can be found in the GenBank/EMBL data libraries under accession numbers BE 640669 to

31 rom this article can be found in the GenBank/EMBL data libraries under accession numbers DU 667459 to

32 Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps e

33 Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps e

34 Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps e

35 Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps e

36 Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Jap

37 Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Jap

38 Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Jap

39 Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Jap

40 bed in this paper have been submitted to the EMBL data library under accession nos. AJ0223728 and AF0

41 ce tool that employs CORBA servers to access EMBL data, and distributes the data in XML format via a

42 The major contributors to the EMBL database are individual authors and genome project

43 The major contributors to the EMBL database are individual authors and genome project

44 Major contributors to the EMBL database are individual scientists and genome proje

45 Sequence alignment with EMBL database entries revealed identity to the published

46 e-fly using sequences directly retrieved via EMBL database queries, or by entering or uploading user

47 A homology search of the GenBank/EMBL database revealed that the amino acid sequence of t

48 A search of the EMBL database revealed that the sequences of the two sub

49 inst (i) all gene sequences from the GenBank-EMBL database, (ii) six A. actinomycetemcomitans, one B.

50 lones did not match sequences in the GenBank/EMBL database, indicating that they may be novel genes.

51 FASTA and Smith-Waterman) on a subset of the EMBL database.

52 ysed 998 Arabidopsis intron sequences in the EMBL database.

53 ches for homologous sequences in the GenBank/EMBL databases have revealed that: (a) the open-ended OR

54 f this clone and comparison with the GenBank/EMBL databases indicated that it did not match any genes

55 sequence homology search of the GenBank and EMBL databases revealed that the amino terminus of LgtF

56 ced and compared with entries in the GenBank/EMBL databases.

57 distinct alleles of the IRAK-4 gene (GenBank/EMBL/DDBJ accession nos. AF445802 and AY186092).

58 Swiss-Prot, in turn, relies on GenBank/Embl/DDJP for predicted proteins from complete genomes o

59 The Cancer Genome Atlas (TCGA) (n = 414) and EMBL-EBI (n = 53), CLEAR score demonstrated both superio

60 have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset

61 arch across the databases available from the EMBL-EBI and to explore the network of cross-references

62 Data are deposited in the appropriate EMBL-EBI archives, including the European Nucleotide Arc

63 an is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at

64 EMBL-EBI is in an ideal position to address these challe

65 Since 2009 the EMBL-EBI Job Dispatcher framework has provided free acce

66 The EMBL-EBI provides access to various mainstream sequence

67 tivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and

68 tivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and

69 Since 2009 the EMBL-EBI provides free and unrestricted access to severa

70 ata flows and further integration with other EMBL-EBI resources for the representation of multi-omics

71 perimental variables and data resided in the EMBL-EBI resources.

72 rces described here can be accessed from the EMBL-EBI website: http://www.ebi.ac.uk.

73 Here, we describe how the EMBL-EBI's biomolecular databases are evolving to cope w

74 public resources and provide an overview of EMBL-EBI's database collection to complement the reviews

75 nome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of

76 d query, EBIMed retrieves the abstracts from EMBL-EBI's installation of Medline and filters for sente

77 ge analyses in a virtual environment next to EMBL-EBI's vast public data resources.

78 CBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB).

79 ed at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human gene

80 ed at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human gene

81 The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databa

82 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databas

83 y and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training cours

84 The European Bioinformatics Institute (EMBL-EBI) is one of three organizations worldwide that p

85 The European Bioinformatics Institute (EMBL-EBI) is unique in Europe and is one of only two org

86 The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, includi

87 se at the European Bioinformatics Institute (EMBL-EBI) recommended by most journals as a repository f

88 k at EMBL-European Bioinformatics Institute (EMBL-EBI), and we consult extensively with life science

89 e), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interaction

90 re of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.uk) are continually expanding: tota

91 lustrate this with examples from our work at EMBL-EBI.

92 earch and access functionalities provided at EMBL-EBI.

93 the database was redesigned and relocated to EMBL-EBI.

94 rogram is available by anonymous ftp at: ftp.embl-ebi.ac.uk under directory /pub/software/unix, file:

95 (threading) are accessible on the web at www.embl-ebi.ac.uk/dali .

96 The databases are available from http://www.embl-ebi.ac.uk/dali/

97 lasslib/ and the EMBL file server http://www.embl-ebi.ac.uk/FTP/index.html

98 e available for academic use from http://www.embl-ebi.ac.uk/holm/nrdb90.

99 logy Laboratory European Nucleotide Archive (EMBL-ENA) and Kabat as well as structure data from the P

100 Data extracted from HGVbase are mapped to EMBL entries to confirm whether the mutation occurs in a

101 equence Database (www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a com

102 The EMBL Nucleotide Sequence Database at the EMBL European Bioinformatics Institute, UK, offers a lar

103 At the EMBL European Bioinformatics Institute, we have develope

104 We work at EMBL-European Bioinformatics Institute (EMBL-EBI), and w

105 ttp://www.cryst.bbk.ac.uk/~classlib/ and the EMBL file server http://www.embl-ebi.ac.uk/FTP/index.htm

106 m the author and has also been placed on the EMBL file server.

107 e 50 000 ESTs in est10.dat (an EST subset of EMBL) finds an error rate of 0.86%, principally due to t

108 ntire expressed sequence tag (EST) subset of EMBL found a contamination rate of 0.27%.

109 o the European Molecular Biology Laboratory (EMBL)/GenBank feature table format for reading and displ

110 notation can be read and written directly in EMBL, GenBank and GFF format.

111 riendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational data

112 other information sources such as PubMed and EMBL/GenBank are provided.

113 or this article have been deposited with the EMBL/GenBank data libraries under accession numbers CB 9

114 d with those of known genes entered into the EMBL/GenBank database.

115 In addition to the DDBJ/EMBL/GenBank feature table format, we share metadata for

116 from over 2700 component sequences from the EMBL/GenBank/DDBJ databases.

117 lated chemokine has been identified from the EMBL/GenBank/DDBJ expressed sequence tag database.

118 ssion of multiple sequence alignment data to EMBL has grown 30-fold in the past 10 years, creating a

119 the European Molecular Biology Laboratory's (EMBL) Heidelberg laboratory and the European Bioinformat

120 ieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

121 From October 12-15th, 2016, EMBOmid R:EMBL held a symposium to bring together those in the sci

122 C. briggsae assembly was accessioned through EMBL, http://www.ebi.ac.uk/services/index.html, using th

123 f the European Molecular Biology Laboratory (EMBL) in Heidelberg, is to ensure that the growing body

124 ry school science teachers within Europe and EMBL member states.

125 BEAUTY searches of the NCBI and EMBL non-redundant protein sequence databases are availa

126 /human gene pairs has been compiled from the EMBL nucleotide database, and their corresponding featur

127 inst the 8400 adult halibut sequences in the EMBL nucleotide database.

128 RNA genes in the taxonomic divisions of the EMBL nucleotide database.

129 The EMBL Nucleotide Sequence Database (www.ebi.ac.uk/embl) a

130 own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

131 own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

132 nst the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

133 nst the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

134 own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

135 ean Nucleotide Archive (ENA), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace

136 The EMBL Nucleotide Sequence Database at the EMBL European B

137 The EMBL Nucleotide Sequence Database constitutes Europe's p

138 The EMBL Nucleotide Sequence Database incorporates, organise

139 The EMBL Nucleotide Sequence Database incorporates, organize

140 The EMBL Nucleotide Sequence Database is a comprehensive dat

141 Information on the EMBL Nucleotide Sequence Database is available at http:/

142 The EMBL Nucleotide Sequence Database is maintained at the E

143 records are distributed daily and the whole EMBL Nucleotide Sequence Database is released four times

144 Data in the EMBL Nucleotide Sequence Database is traditionally avail

145 nstitute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucl

146 The Ensembl Trace Archive and the EMBL Nucleotide Sequence Database, known together as the

147 The EMBL Nucleotide Sequence Database, maintained at the Eur

148 The EMBL Nucleotide Sequence Database, maintained at the Eur

149 The EMBL Nucleotide Sequence Database, maintained at the Eur

150 their own sequences against the data in the EMBL Nucleotide Sequence Database, the complete genomic

151 ion of data from many sources, including the EMBL Nucleotide Sequence Database, the UniProt Knowledge

152 The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database is maintained at the

153 The EMBL Object Model is available at http://corba.ebi.ac.uk

154 can read a pair of DNA sequences in GenBank, Embl or Fasta formats, with or without a comparison file

155 90413 but did not correspond exactly to any EMBL or GenBank database sequence.

156 The EMBL Sequence Version Archive is a new publicly availabl

157 Using a P1 and a lambda EMBL subclone, the chromosomal site of the human AQP4 ge

158 Webin-Align: http://www.ebi.ac.uk/embl/Submission/align_top.html, EMBL-Align: ftp://ftp.eb

159 GENEBANK/EMBL/SWISS PROT database comparison of all sequences rev

160 e flexible and robust parsing and editing of EMBL/SWISS-PROT databases.

161 se group of scientists assembled at the EMBO/EMBL Symposium 'Metabolism in Time and Space' to discuss

162 is study have been submitted to DDBJ/GenBank/EMBL under accession numbers EU940701-EU977132 (FLI cDNA