Translations

Each coding part (annotated with a CDS feature) of each nucleotide sequence must be translated into the appropriate protein. Depending on the organism/sequence source, BiSSAP chooses the appropriate code for the translation. BiSSAP supports all known translation codes.

Each organism name (including user-defined name) is associated with one translation code. Artificial sequences and synthetic constructs are an exception. When a CDS is added to such a sequence, BiSSAP allows you to choose the correct translation code.

BiSSAP adds two qualifiers to each CDS:

  • transl_table - containing the number of the translation table
  • translation - containing the result of the translation, in addition to the generated sequence described below. (This qualifier is added after generating the protein sequence – see below.)

How to translate

Translating a part of the sequence in BiSSAP is very simple:

  1. For a region to be translated, a CDS, which indicates the location of the region, is necessary. If such a CDS does not exist, please create it.
  2. Right-click the sequence to display a local context menu. Select Generate protein.

  3. BiSSAP chooses the translation code depending on the organism name.
  4. After translation, BiSSAP displays a confirmation message.

  5. If there are several CDSs, a feature-selection window appears when you choose one of the two translation commands. Choose the CDSs you want to use for translation. If the sequence has already been generated, you can regenerate it by answering a confirmation question.

  6. The operation generates the translated protein sequence or sequences (depending on the number of CDSs). The translated sequences have order numbers consecutive to the parent sequence. Other sequences are renumbered to accommodate this. The dialog shows the numbers the generated sequences will have.

The operation also adds the translation qualifier to each translated CDS feature.

Generated sequences

The generated sequences are clearly marked in the Sequence Browser.

Generated sequences are treated differently from normal sequences:

  • You cannot edit the sequence itself. You have to edit either the parent sequence, or the parent CDS, and then regenerate the sequence. You can, however, add/edit features.
  • When a parent sequence or CDS is edited, the program asks if it should regenerate the dependent sequences.
  • A generated sequence is deleted when the parent sequence or the parent CDS is deleted.