Sequences 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

Creating a new sequence

  • Select a project in the Project Browser. Expand it so that you can see the Sequences list. Right-click the list. Select Sequences -> Create Sequence from the pop-up menu.

  • The Create Sequence dialog is displayed. The required fields are marked with a red triangle.

  • You can only fill in some fields after you have selected other fields, e.g. you can start filling in sequences only after you have selected the molecule type.
  • The molecule code depends on the type of molecule.
    • For nucleotides, like DNA, RNA, etc., the IUPAC code is used (http://www.iupac.org )
    • For proteins, the one-letter code is used. However, you can click the button Insert 3-letter code and type or paste in the three-letter code.
  • The organism field suggests the correct scientific names. You are encouraged to choose one of the suggestions. If you want to use a name for a new organism that does not exist in BiSSAP, the application will ask you to add a new organism to the taxonomy database (see Taxonomy)
  • Additional Sequence Description is optional, except for artificial sequences or synthetic construct when it becomes mandatory. The content will be put in the note qualifier in the source feature.
  • Click Create sequence to complete the operation, or Cancel to cancel it.

Insert Before and Insert After

The sequence created as described in the previous paragraph will be the last one in the current sequence listing. There are two ways to create sequence listings in other places:

  • Insert Before
  • Insert After

To create a sequence before a specific position:

  • Right-click the sequence in the Sequence Browser.
  • Choose Insert Sequence Before

  • The next steps are the same as for standard sequence creation.

To create a sequence after a specific position:

  • Right-click the sequence in the Sequence Browser.
  • Choose Insert Sequence After

  • The next steps are the same as for standard sequence creation.

Creating an empty sequence

To create an empty sequence:
* Select a project in the Project Browser. Expand it so that you can see the Sequences list.
* Right-click the list. Select Sequences -> Create Sequence Without Residues from the pop-up menu.

An empty sequence will be created.

You can also replace an existing sequence with an empty one in a single step. To do this, select a project in the Project Browser, right-click the sequence in the Sequence Browser and then choose Replace sequence with sequence without residues.

Creating all empty sequences needed to fill the gaps

If there are gaps in the project, empty sequences will be created automatically in the process of generating a sequence listing. No additional action is required.

Creating a generated sequence

See Translations.

Artificial sequences

Artificial sequences are treated separately. When you enter artificial in the organism field, Additional sequence description becomes mandatory. The content will be put in the note qualifier in the source feature.

Note:

  • The application prevents you from typing in incorrect characters as sequence data.
  • You can paste in a copied sequence.
  • Clicking on Reformat Sequence has two functions:
    • it removes unsupported characters (counters, invalid characters, etc.) which can be copied and pasted from another source.
    • it groups the characters, making them more presentable.
  • The default input format for protein sequences is the one-letter code. However, you can click the button 3-letter code and type or paste in the three-letter code.

Editing sequences

To edit a sequence, start the sequence editor.

  • Select a the project in the Project Browser. The sequences will load into the Sequence Browser.
  • Right-click the sequence you want to edit. Select Sequences -> Edit Sequence from the pop-up menu.
  • The editor will open, with the data loaded. Modify the data as necessary.
  • The required fields are marked with a red triangle. All other fields are optional. For details, see the section Creating a new sequence.
  • Save your data by pressing Crtl-S (Command-S, if you are working with Mac OS X).
  • You can close the editor without saving (you will be asked to confirm that this is indeed your intention).

Deleting sequences

To delete a sequence:

  • Select a project in the Project Browser. The sequences will load into the Sequence Browser.
  • Right-click the sequence you want to delete. Select Sequences -> Remove Sequence from the pop-up menu.

  • Answer yes to delete the sequence, no to cancel.

Deleting all sequences

To delete all the sequences from a project:

  • Select a project in the Project Browser. Expand the tree so that you can see Sequences list.
  • Right-click the Sequences list. Select Remove All Sequences from the pop-up menu.

  • Answer yes to delete the sequences, no to cancel.

Importing sequences

You can import a sequence in different formats. This feature is designed to help you to build sequence listings from sequences generated by other software.

You can import one or more sequences from a file.

For this kind of import, BiSSAP supports the following formats:

  • ST.25
  • XML
  • FASTA
  • EMBL

For patent formats like ST.25 or XML, the difference between sequence import and loading sequence listing is:

  • during loading sequence listing, a new project is created in BiSSAP
  • during import, the sequences are assigned to an existing project

To import a sequence:

  • Right-click Sequences in the Project Browser.

  • Select Sequences and then Import Sequence From A File.
  • A dialog opens. First select the type of file from which you wish to import the sequence.

  • Select whether to import one sequence or all sequences from the file.
  • Select the file.

  • The sequences are imported into the project.

Exporting sequences

You can export a sequence in different formats. This feature is designed to help you to use a sequence from a sequence listing in other software, including software that does not support ST.25 or the sequence listing XML format.

You can export only one sequence at a time.

For this kind of export, BiSSAP supports the following formats:

  • ST.25
  • XML
  • FASTA
  • EMBL

For formats like ST.25 or XML, the difference between sequence export and generating a sequence listing is:
when a sequence listing is being generated, only formats like ST.25 and XML are available. The project is verified, and the complete sequence listing is generated. During export, however, only the scientific data is exported. Patent-related information is not exported.

To export a sequence:

  • Select a project in the Project Browser
  • Right-click a sequence in the Sequence Browser.

  • Select Export Sequence To A File

  • A dialog opens. First select the type of the file to which you wish to export the sequence.

  • Select the file.

  • The sequence is written to the file.