Assembled and annotated sequences

The main format for for assembled and annotated sequences is the flat file format, which is defined in full detail in the ENA Assembled Sequence User Manual. Assembled and annotated sequences are available in flat file and other formats, namely Fasta and XML, through the ENA Browser. Details on ENA's assembled and annotated sequences release can be found in the release notes. The feature annotation usage and interpretation is defined in the INSDC Feature Table Document, which is also made available through the Feature Table Browser.

Data classes

Please refer to the table below for a summary of data classes. The 'Example' column contains example entries retrieved from the ENA Browser in HTML, XML, Fasta, and flat file formats. The ENA Browser provides retrieval and visualisation functionality over ENA data and metadata and uses REST URLs to support both interactive and programmatic access. Please note that all assembled and annotated sequences use the same flat file format and are constrained by the same XML Schema: ENA.embl.xsd. Please also note that all XML documents returned by the ENA Browser are included in and validate against the ENA.root.xsd XML Schema.

Data class Definition Example
EST Raw expressed sequence tags without sequence quality information Fasta
Flatfile
HTML
XML
WGS Genomic contigs Fasta
Flatfile
HTML
XML
GSS Genome survey sequence; single pass, single direction sequence Fasta
Flatfile
HTML
XML
HTC High throughput assembled transcriptomic sequence and optional annotation Fasta
Flatfile
HTML
XML
HTG High throughput assembled genomic sequence and optional annotation Fasta
Flatfile
HTML
XML
STD Assembled and annotated sequences Fasta
Flatfile
HTML
XML
CON Scaffolds build from genomic or transcriptomic contigs Fasta
Flatfile
HTML
XML
STS Sequence tagged site Fasta
Flatfile
HTML
XML
PAT Patent sequences Fasta
Flatfile
HTML
XML
TSA Transcriptomic contigs Fasta
Flatfile
HTML
XML
CDS Coding sequences Fasta
Flatfile
HTML
XML

Latest ENA news

11 Oct 2017: Read data download issues resolved

Read data download issues previously affecting ftp.sra.ebi.ac.uk and fasp.sra.ebi.ac.uk services now resolved.

06 Oct 2017: ENA read data download issues

Issues with read data download from ftp.sra.ebi.ac.uk and fasp.sra.ebi.ac.uk

04 Oct 2017: ENA Release 133

Release 133 of ENA's assembled/annotated sequences now available