Sequence Annotation (SA)

Knowledge associated with specific coordinates on a biological sequence is referred to as a sequence annotation. Subtypes include genome annotations, gene annotations, and reference annotations (among others). Sequence annotations are used to represent concepts such as gene models, alternatively spliced transcripts, and coding regions. Untranslated regions, introns, pseudogenes, regulatory regions, and repetitive sequences are also frequently represented as features mapped to a coordinate system. In addition to serving as a guide for which sequences correspond to which genes and transcripts, sequence annotations are also used to represent the parts of a sequence (e.g. coding sequence, exons, splice junctions, etc.) and how those parts relate to each other.

The Sequence Annotation (SA) study group is evaluating interoperability gaps in:

• the annotation of biological sequence;
• the representation of sequence features (i.e. genes, transcripts, exons, etc.);
• the storage, transformation, and transmission of sequence annotations between annotation providers and users.

The work carried out by the SA study group aims to inform the future development of an extensible, common model for describing specific genomic regions of interest.