Sequence types
There are three kinds of sequence in BiSSAP:
- standard sequences
- generated sequences
- sequences without residues, also called “zero”, “000”, “skip code” or “empty” sequences
Standard sequences
For the purpose of this document, a sequence which is neither generated nor empty is a standard sequence.
A standard sequence in BiSSAP has the following properties:
- Description - this is a description used internally in BiSSAP. It helps you to manage your sequences. It is not exported into standard sequence listings (with the exception of drafts).
- Sequence number - position of the sequence in the file. All sequences in the final file must have consecutive numbers without gaps.
- Organism - the source of the sequence. This data is required for each sequence. See Taxonomy.
-
Molecule type - the type of molecule of which the sequence is composed
(see Molecule Types).
Depending on the molecule type:
- different sets of symbols (codes) for representing residues are used for sequence data
- different sets of features can be assigned
- different verification rules are applied
- Sequence data - the biological sequence itself. The code for representing residues depends on the molecule type. See Nucleotides and Amino Acids.
A sequence can be annotated with features.
Generated sequences
A generated sequence is a protein sequence created from the nucleotide sequence by means of translation.
A generated sequence has certain restrictions:
- The sequence data, organism, etc., cannot be edited. Changes can only be made by editing either the original sequence or the CDS.
- The sequence can be regenerated when the data on which it is based (like the sequence, CDS) is modified.
- The sequence is automatically removed when the data on which it depends is deleted.
The following qualifiers in the “source” feature of the original sequence are transferred to the “source” feature of the generated sequence:
- mol_type
- organism
- note
- db_xref.
“000” sequences (empty)
This is a special type of sequence. It has an order number but none of the other properties of a standard sequence, i.e. it has no features, organism names, etc. It has the symbolic string “000”, which means “no data” instead of normal sequence data.
According to the rules,
- the sequence numbering must be preserved
- there may be no gaps in numbering
You cannot upgrade an empty sequence to a standard sequence. You cannot edit empty sequences or add features or qualifiers to them.
Note:
To replace an empty sequence with a standard one, you have to:
- delete the empty sequence
- create a standard sequence
- re-order the sequences so that the new sequence has the number of the deleted empty sequence
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