The EMBL Nucleotide Sequence Database

By Carola Kanz, Philippe Aldebert, N. Althorpe, W. Baker, A. Baldwin, Kirsty Bates, P. Browne, Alexandra van den Broek, Matias Castro, Guy Cochrane and 22 more. Nucleic Acids Res., 2004

1,060 citations recorded by the source corpus.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences and annotation from available public sources. The database is part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged daily between the collaborating institutes to achieve swift synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation (TPA) and alignments. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. New and updated data records are distributed daily and the whole EMBL Nucleotide Sequence Database is released four times a year. Access to the sequence data is provided via ftp and several WWW interfaces. With the web-based Sequence Retrieval System (SRS) it is also possible to link nucleotide data to other specialist molecular biology databases maintained at the EBI. Other tools are available for sequence similarity searching (e.g. FASTA and BLAST). Changes over the past year include the removal of the sequence length limit, the launch of the EMBLCDSs dataset, extension of the Sequence Version Archive functionality and the revision of quality rules for TPA data.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/782d8e30d599e1499555268b5b97c4a86b6bc25b

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras (2006, background): “Recent papers (2, 14) have reported numerous corrupt 16S rRNA gene sequences within the public repositories (3, 16 , 19), and it has been estimated that overall, 5% of records are likely to have substantial anomalies (2).”
IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences (2005, methodology): “Prior to being entered in IMGT/LIGM-DB, IG and TR sequences must be submitted to EMBL, GenBank or DDBJ, in order to get a unique accession number which is also the entry identifier in IMGT/LIGM-DB.”
GPCRdb: an information system for G protein-coupled receptors (2015, methodology): “The GPCRDB contains sequences, mutation and ligand binding data that are regularly imported from the original sources [SWISS-PROT (4), EMBL ( 5 ), TinyGRAP (6)].”
Marker-Assisted Plant Breeding: Principles and Practices (2015, methodology): “In addition, tools like FASTA and BLAST are also available (Kanz et al. 2005).”
IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex (2003, methodology): “Both the IMGT/HLA and IMGT/MHC databases are based upon sequences currently found in the EMBL Nucleotide Sequence Database (EMBL) ( 5 ), GenBank (6) and the DNA DataBank of Japan (DDBJ) (7).”
MRS: a fast and compact retrieval system for biological data (2005, background): “The MRS server allows for very rapid queries in a large number of flat-file data banks, such as EMBL, UniProt, OMIM, dbEST, PDB, KEGG, etc.”
The IMGT/HLA database (2008, background): “It must be noted that all sequences within the IMGT/HLA database should also be available from the more general nucleotide sequence databases: EMBL-Bank (24,25), GenBank (26) and the DNA Database of Japan (DDBJ) (27,28).”
Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies (2016, methodology): “In situations without non-genetic effects, we also examined the effect of including PCs as covariates using a human population dataset[38].”
The integrated microbial genomes (IMG) system (2005, background): “This requires a high level of genome diversity from public sources, such as EBI’s Genome Reviews (6), NCBI’s RefSeq (7) and EMBL’s Nucleotide Sequence Database (8).”
The Sequence Ontology: a tool for the unification of genome annotations (2005, background): “Kulikova T, Aldebert P, Althorpe A, et al.: The EMBL Nucleotide Sequence Database.”
GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding (2021, methodology): “To illustrate the distribution of species coverage, we used the European Nucleotide Archive (ENA) (Kanz et al., 2005) (release 138, FIGURE 1 Illustration of the process for generating map and data in the GAPeDNA web application (a) and details on the interface (b).”
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks (2008, background): “Enhanced with Gene Ontology (GO) annotations (31), KEGG pathways (21), nucleotide and amino acid sequences from UniProt (32), DDBJ (33), EMBL ( 34 ) and GenBank (35); links to NCBI Entrez-Gene pages (14); and microarray reports from the EDGE database (36).”
The Universal Protein Resource (UniProt): an expanding universe of protein information (2005, neutral): “GenBank/EMBL/DDBJ (11)], model organism genomes [e.”
GenBank: update (2004, background): “GenBank incorporates sequences submitted to the EMBL Data Library (2) in the UK and the DNA Data Bank of Japan (DDBJ) (3) as part of a long-standing international collaboration between the three databases in which data is exchanged daily to ensure a uniform and comprehensive collection of sequence i”