ENA Sequence Flat File Format
Countries that developed this resource Austria , Belgium , Croatia , Czech Republic , Denmark , Finland , France , Germany , Greece , Hungary , Iceland , Israel , Italy , Lithuania , Luxembourg , Malta , Montenegro , Netherlands , Norway , Portugal , Republic of Ireland , Slovakia , Spain , Sweden , Switzerland , United Kingdom
Created in 1980
How to cite this record FAIRsharing.org: ENA Sequence Flat File Format; ENA Sequence Flat File Format; DOI: https://doi.org/10.25504/FAIRsharing.q9nh66; Last edited: Feb. 26, 2020, 11:54 a.m.; Last accessed: Jan 20 2021 4:06 p.m.
Record updated: Feb. 26, 2020, 11:54 a.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.q9nh66' by 'The FAIRsharing Team' at 11:54, 26 Feb 2020 (not approved): 'miriam_id' has been modified: Before: After: None
Edits to 'https://fairsharing.org/FAIRsharing.q9nh66' by 'The FAIRsharing Team' at 11:50, 26 Feb 2020 (approved): 'supportLinks' has been modified: Before: After: help|https://www.ebi.ac.uk/ena/submit/flat-file help|https://www.ebi.ac.uk/ena/WebFeat/ help|https://www.ebi.ac.uk/ena/submit/sequence-format Added: help|https://www.ebi.ac.uk/ena/submit/flat-file help|https://www.ebi.ac.uk/ena/WebFeat/ help|https://www.ebi.ac.uk/ena/submit/sequence-format Removed: 'name' has been modified: Before: EMBL sequence format After: ENA Sequence Flat File Format 'related_standards' has been modified: Before: ENA Sequence XML Schema After: Added: Removed: ENA Sequence XML Schema 'onto_domains' has been modified: Before: Sequence deoxyribonucleic acid genome After: Nucleic acid sequence Sequence deoxyribonucleic acid genome Added: Nucleic acid sequence Removed: 'contactEmail' has been modified: Before: email@example.com After: firstname.lastname@example.org 'contact' has been modified: Before: Data Submissions at EBI After: EBI Helpdesk 'shortname' has been modified: Before: EMBL sequence format After: ENA Sequence Flat File Format 'homepage' has been modified: Before: ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt After: ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt 'description' has been modified: Before: EMBL sequence format is a standardised plain text format for nucleotide sequences. After: ENA Sequence Flat File Format is a standardised plain text format for nucleotide sequences. This format was previously called the EMBL Sequence Flat File Format.
Edits to 'https://fairsharing.org/FAIRsharing.q9nh66' by 'The FAIRsharing Team' at 09:29, 07 Jun 2019 (approved): 'organizations' has been modified: Before: After: European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains Added: European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains Removed:
Edits to 'https://fairsharing.org/FAIRsharing.q9nh66' by 'The FAIRsharing Team' at 23:31, 19 May 2019 (approved): 'taxonomies' has been modified: Before: After: All Added: All Removed: 'homepage' has been modified: Before: http://www.bioperl.org/wiki/EMBL_sequence_format After: ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt 'description' has been modified: Before: EMBL sequence format After: EMBL sequence format is a standardised plain text format for nucleotide sequences. 'countries' has been modified: Before: After: United Kingdom Added: United Kingdom Removed:
Edits to 'https://fairsharing.org/FAIRsharing.q9nh66' by 'The FAIRsharing Team' at 22:56, 19 May 2019 (approved): 'miriam_id' has been modified: Before: None After: 'description' has been modified: Before: After: EMBL sequence format
Conditions of UseApplies to: Data use
No publications available
No guidelines defined
No semantic standards defined
Models and Formats
No identifier schema standards defined
No metrics standards defined
This project aims to support the international Aspergillus research community by gathering all genomic information regarding this significant genus into one resource - The Central Aspergillus REsource (CADRE). CADRE facilitates visualisation and analyses of data using the Ensembl software suite. Much of our data has been extracted from Genbank and augmented with the consent of the original sequencing groups. This additional work has been carried out using both automated and manual efforts, with support from specific annotation projects and the general Aspergillus community.
Integrated Microbial Genomes And Microbiomes
The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a set of publicly available genome and metagenome datasets. IMG/M is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and microbiome datasets, as long as they agree with the IMG/M data release policy and follow the metadata requirements for integrating data into IMG/M.
This resource is a hierarchical clustering of UniProt protein sequences into hierarchical trees. This resource allows for the study of sub-family and super-family of a protein, using UniRef50 clusters.
Death Domain Database
Death Domain Database is a manually curated database of protein-protein interactions for Death Domain Superfamily.
MitoZoa is a specialized database collecting complete and nearly-complete (longer than 7 kb) mtDNA entries of metazoan species, excluding Placozoa. MitoZoa contains curated entries, whose gene annotation has been significantly improved using a semi-automatic reannotation pipeline and by manual curation of mitogenomics experts. MitoZoa has been specifically designed to address comparative analyses of mitochondrial genomic features in a given metazoan group or in species belonging to the same genus (congeneric species). MitoZoa focuses on mitochondrial gene order, non-coding regions, gene content, and gene sequences.
PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as well as providing structural and functional annotation and access to large-scale data sets.
CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.
European Nucleotide Archive
The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data, the ENA provides a portfolio of services for submission, data management, search and retrieval across web and programmatic interfaces. The ENA is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis.
Patent Data Resources
Patent data resources at the EBI contain patent abstracts, patent chemical compounds, patent sequences and patent equivalents. Multiple sets of patent sequences are available at EBI. Patent proteins cover sequences of EPO (European Patent Office) proteins, JPO (Japan Patent Office) proteins, KIPO (Korean Intellectual Property Office) proteins and USPTO (United States Patent and Trademark Office) proteins. Patent nucleotides contain the patent class data in the EMBL-Bank. Non-redundant patent sequences consist of 2 levels databases. Level-1 non-redundant patent sequences are 100% identical over the same length; Level-2 non-redundant patent sequences are identical and belong to a same patent family (a same invention).
Integrated resource of protein families, domains and functional sites
InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium.
Description of Plant Viruses
DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. The database will not be updated with sequence or taxonomic data from Aug 2013.
Pseudomonas Genome DB
The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.
miRBase Sequence Database
The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. The miRBase Registry continues to provide gene hunters with unique names for novel miRNA genes prior to publication of results. The miRBase Targets database is a new resource of predicted miRNA targets in animals.
Eukaryotic Promoter Database
The Eukaryotic Promoter Database (EPD) provides accurate transcription start site (TSS) information for promoters of 15 model organisms, from human to yeast to the malaria parasite Plasmodium falciparum. While the original database was a manually curated database based on published experiments, new promoter collections are now produced entirely automatically (under the name “EPDnew”) based on high-throughput transcript mapping data and high-quality gene annotation resources. Corresponding functional genomics data can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats like FASTA or BED for subsequent analysis with other tools; of note, EPD is tightly integrated with two tool suites developed by our group: ChIP-Seq (https://ccg.epfl.ch/chipseq) and Signal Search Analysis (https://ccg.epfl.ch/ssa), for analysis of chromatin context and sequence motif respectively. EPD provides promoter viewers, designed with the aim of integrating and displaying information from different sources about, for instance, histone marks, transcription factor-binding sites or SNPs with known phenotypes. These viewers rely upon the UCSC genome browser as a visualization platform, which enables users to view data tracks from EPD jointly with tracks from UCSC or public track hubs.
BCCM/GeneCorner Plasmid Collection
The BCCM/GeneCorner Plasmid Collection warrants the long-term storage and distribution of plasmids, microbial host strains and DNA libraries of fundamental, biotechnological, educational or general scientific importance. The focus is on the collection of recombinant plasmids that can replicate in a microbial host strain. BCCM/GeneCorner also accepts natural and genetically modified animal or human cell lines, including hybridomas, as well as other genetic material, in the safe deposit and patent deposit collections.
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European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute) Lead