3  a3 Format

The Amino Acid Annotation (a3) format is created to hold amino acid sequences and annotations.

An example of the a3 format is shown below:

The a3 format example showing the nested list structure of annotations.

Figure 3.1

It is a nested list of lists. At the top level, there are:

• Sequence A character vector containing the amino acid sequence.
• Annotations A named list of lists containing different types of annotations.
• UniprotID A character containing the Uniprot ID of the protein if available.
• Reference A URL of a relevant publication if available.

3.1 Annotations

There are 5 different annotation types defined in the a3 format, and more can be added as needed.

• Site A named list of (unsigned) integer vectors. The name gives the type of annotation, and the vector contains the amino acid positions of the annotation.
• Region A named list of integer vectors. The name gives the type of annotation, and the vector contains the start and end positions of the annotation.
• PTM A named list of integer vectors with positions for each PTM.
• Cleavage Sites A named list of integer vectors with positions for each cleavage site.
• Variant A list of lists with variant information. Each element list can contain any number of named elements for the given variant.