Managing Features

General information

Feature properties

Each feature has at least the following:

• feature key - a word indicating the function of the feature, like CDS or misc_feature (see the list of available feature keys)
• location - the location identifies the part of the sequence to which the f eature applies. For more detailed information, see the section on locations
• qualifiers - information about the feature

For more detailed information about features, see http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html or http://www.ebi.ac.uk/embl/WebFeat/index.html

Creating features

• Select a project in the Project Browser. The sequences will load into the Sequence Browser.
• Expand the sequence to which you want to add a feature. Right-click on Features. Select Create Feature from the pop-up menu.

  

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

  

• Some fields can only be completed once other fields have been selected.
• The input range for many fields is restricted, depending on the values chosen in other fields. There is a separate list of allowed feature keys for nucleotides and features.

  

• The qualifier list is feature-specific.

  

• Click Create feature to complete the operation or Cancel to cancel it.

  

Creating CDS feature

When you create a CDS feature for a sequence which is an artificial sequence or a synthetic construct, BiSSAP allows you to define one translation table per CDS.

See Translations.

Creating protein features

The feature for protein sequences is created in the same way as for nucleotide sequences.

The feature-key list is protein-specific. For a description of the protein list, see here.

There is just one qualifier for all protein keys. This qualifier does not have a name. It is referred to as description field in Uniprot, and in BiSSAP – as usual – as Qualifier value.

In some cases this unnamed qualifier is mandatory.

Editing features

• Select a project in the Project Browser. The sequences will load into the Sequence Browser.
• Expand the sequence, and then the Features list to see the feature you want to edit. Right-click the feature, then select Edit Feature from the pop-up menu.

  

• The feature editor opens.

Deleting features

To delete a feature:

• Select a project in the Project Browser. The sequences will load into the Sequence Browser.
• Expand the sequence and then the Features list to see the feature you want to delete. Right-click the feature, then select Remove Feature from the pop-up menu.
• Answer yes to remove the feature, no to cancel.

If you delete a CDS feature, generated sequences depending on that feature will also be removed.

Removing all features

To remove all features from a sequence in a single operation:

• Select a project in the Project Browser. The sequences will load into the Sequence Browser.
• Expand the sequence so that you can see the Features list you want to delete. Right-click the feature, then select Remove All Features from the pop-up menu.