Creating a new sequence
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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.
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The Create Sequence window 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 )
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For proteins, the default input format is one-letter code. However if you have the sequence represented in 3-letter code, you can click the button Insert 3-letter code and type or paste in the three-letter code.
Note: The button Insert 3-letter code is enabled only if you have already set the Molecule type to PRT.
- 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 sequences with artificial or unknown source when it becomes mandatory. You can enter in this field max. 260 characters. 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.
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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.
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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.
Generating the protein sequence corresponding to a CDS feature
See Translations.
Artificial sequences
When you enter Artificial Sequence 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.
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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.
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