Literature DB >> 10592171

The EMBL nucleotide sequence database.

W Baker1, A van den Broek, E Camon, P Hingamp, P Sterk, G Stoesser, M A Tuli.   

Abstract

The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (http://www.ebi.ac. uk/embl/index.html ) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank (USA). Data is exchanged amongst the collaborative databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. WEBIN is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via Internet and WWW interfaces. EBI's Sequence Retrieval System (SRS) is a network browser for databanks in molecular biology, integrating and linking the main nucleotide and protein databases plus many specialised databases. For sequence similarity searching a variety of tools (e.g., BLITZ, FASTA, BLAST) are available which allow external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

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Year:  2000        PMID: 10592171      PMCID: PMC102461          DOI: 10.1093/nar/28.1.19

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  7 in total

1.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

2.  SRS: information retrieval system for molecular biology data banks.

Authors:  T Etzold; A Ulyanov; P Argos
Journal:  Methods Enzymol       Date:  1996       Impact factor: 1.600

3.  Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.

Authors:  T Heinemeyer; E Wingender; I Reuter; H Hermjakob; A E Kel; O V Kel; E V Ignatieva; E A Ananko; O A Podkolodnaya; F A Kolpakov; N L Podkolodny; N A Kolchanov
Journal:  Nucleic Acids Res       Date:  1998-01-01       Impact factor: 16.971

4.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998.

Authors:  A Bairoch; R Apweiler
Journal:  Nucleic Acids Res       Date:  1998-01-01       Impact factor: 16.971

5.  Using the FASTA program to search protein and DNA sequence databases.

Authors:  W R Pearson
Journal:  Methods Mol Biol       Date:  1994

6.  Finding flexible patterns in unaligned protein sequences.

Authors:  I Jonassen; J F Collins; D G Higgins
Journal:  Protein Sci       Date:  1995-08       Impact factor: 6.725

7.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors:  J D Thompson; D G Higgins; T J Gibson
Journal:  Nucleic Acids Res       Date:  1994-11-11       Impact factor: 16.971

  7 in total
  33 in total

1.  Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms.

Authors:  M Derakshani; T Lukow; W Liesack
Journal:  Appl Environ Microbiol       Date:  2001-02       Impact factor: 4.792

2.  RHdb: the Radiation Hybrid database.

Authors:  P Rodriguez-Tomé; P Lijnzaad
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

3.  The European Large Subunit Ribosomal RNA Database.

Authors:  J Wuyts; P De Rijk; Y Van de Peer; T Winkelmans; R De Wachter
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

4.  The RDP-II (Ribosomal Database Project).

Authors:  B L Maidak; J R Cole; T G Lilburn; C T Parker; P R Saxman; R J Farris; G M Garrity; G J Olsen; T M Schmidt; J M Tiedje
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

5.  The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments.

Authors:  J Murvai; K Vlahovicek; E Barta; S Pongor
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

6.  GOBASE: the organelle genome database.

Authors:  N Shimko; L Liu; B F Lang; G Burger
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

7.  ICB database: the gyrB database for identification and classification of bacteria.

Authors:  K Watanabe; J Nelson; S Harayama; H Kasai
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

8.  IMGT/HLA Database--a sequence database for the human major histocompatibility complex.

Authors:  J Robinson; M J Waller; P Parham; J G Bodmer; S G Marsh
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

9.  Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems.

Authors:  F Horn; G Vriend; F E Cohen
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

10.  HOBACGEN: database system for comparative genomics in bacteria.

Authors:  G Perrière; L Duret; M Gouy
Journal:  Genome Res       Date:  2000-03       Impact factor: 9.043

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