Exploring an EMBL-Bank entry
Overview of an EMBL-Bank entry
EMBL-Bank provides an easy-to-read view of the data, where information such as taxonomy and annotation features are grouped into separate sections. In addition there is a graphical view of assembly and annotation features. EMBL-Bank also has a plain text view that is useful for programmatic access (Figure 33).
Figure 33. EMBL-Bank entry for BN000065; on the left is the default view and on the right the plain text view.
EMBL-Bank entry - General summary section
The top of an EMBL-Bank entry provides a general summary of the data, the ability to change the view of the entry and to download information (Figure 34).
Figure 34. EMBL-Bank entry BX548174 displaying general entry information.
EMBL-Bank entry - Navigation section
EMBL-Bank provides cross-references to almost forty other databases, including Ensembl, UniProtKB, InterPro, RFAM, WormBase, GrainGenes, dictyBase, FlyBase, VectorBase, GOA, PDB and IMGT/HLA. An entry will contain links to the external database(s) that have information on the sequence, providing a valuable source of additional annotation (Figure 35).
Figure 35. EMBL-Bank entry BX548174 showing Navigation section (DR line); each cross-reference has a link to the relevant database entry, such as the RNA database Rfam.
EMBL-Bank entry - Overview section
The overview section provides an at-a-glance graphical display of the assembly and annotation features of the sequence (Figure 36). Annotation features describe where genes, mRNA, exons, introns, CDS (coding sequence) and other features are located on the sequence. This information is supplied by the author, or occasionally as third party annotation (see section 'How is the sequence annotated').
EMBL-Bank entry - Source features section
The source features section details where the sequence came from (Figure 37). For more information please see the section on 'How to search ENA with taxonomy'.
Figure 37. EMBL-Bank entry Z71230 showing the Source Feature(s) section.
EMBL-Bank entry - Other features section
In addition to the graphical display of the annotation features we saw in the Overview section, EMBL-Bank also provides a detailed description of each feature in the 'Other Feature(s)' section (Figure 38). There are over fifty different features that can provide annotation for a sequence, and over seventy different qualifiers that help refine these features. Which features are described in a particular entry depends on the data the author submitted (ENA curators do not add features; they are provided by either the author or by third party annotation).
Figure 38. EMBL-Bank entry BN000065 showing the Other Feature(s) section.
EMBL-Bank entry - References section
Literature references relating to the submitted sequence, including third party annotation, are provided in the reference list (Figure 39). Cited literature should be considered as a pointer to scientific information and not a credit for the elucidation of the sequence.
Figure 39. EMBL-Bank entry BN000065 showing the reference section.
EMBL-Bank entry - Sequence section
Either the full or part of the sequence can be viewed in FASTA format (Figure 40).
Figure 40. EMBL-Bank entry showing the sequence section.