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 names) is associated by default with one translation code. When a CDS is added to such a sequence, BiSSAP allows you to choose an alternative translation code if necessary.

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 as given in the CDS feature.
  4. After translation, the amino acid sequence corresponding to the CDS feature is appended at the end of the current list of sequences and BiSSAP displays a confirmation message.

  5. If there are several CDSs, a feature-selection window appears when you choose the translation command.

  6. 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.

  7. The operation generates the translated protein sequence or sequences (depending on the number of CDSs) and appends them at the end of the current list of sequences.

Amino acid sequences corresponding to CDS features

The amino acid sequences generated in relation to CDS features are clearly marked in the Sequence Browser.

Such 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 BiSSAP will automatically regenerate the amino acid sequence(s) corresponding to the CDS. You can, however, add/edit features.
  • When a parent sequence or CDS is edited, the program regenerates the dependent sequences.
  • An amino acid sequence corresponding to a CDS feature is deleted when the parent sequence or the parent CDS is deleted.