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FAQ: Using unsupported feature types 
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Joined: Tue Feb 08, 2011 8:23 pm
Posts: 19
Post FAQ: Using unsupported feature types
Annotations in sequence files created in other applications or in very early versions of MacVector are not displayed properly.

Early versions of MacVector (before version 6.5) allowed the creation of feature types, such as 'frag' that are no longer supported. For example, PCR primers might be annotated as 'frags' so that they would display on the annotated sequence maps. However, these features are not displayed on the annotated display in the current version on MacVector. How do I get frags to appear in the annotated display?

Existing sequences with unsupported features may be edited to change those features to a supported type.

MacVector no longer supports certain feature types, such as 'frag'. The 'frag' feature type is ONLY created as a result of copy and paste operations within MacVector; you can't manually create this feature type. This will affect your working habits since you will have to pick a new feature type for future work. Here are two methods that can be used to display 'frag' features:

Option 1. Display 'frag' features in the graphic map rather than the annotated display.

1. Open the desired sequence, perform a restriction analysis, and select the Restriction Map display option.

2. When the Cut Site Map opens, click the Zoom To Residue Level button in the Graphics Palette to see all the letters (or set the residues/line value to 60).

3. Turn on the 'frag' feature, and turn off any unwanted feature types via their check boxes.

4. Adjust the residues-per-line and line length settings as necessary.

5. You can double-click on the 'frag' line in the Graphics Palette to open the Symbol Editor and assign 'frag' to a more appropriate symbol style, e.g. single- or double-ended arrow, as desired.

Note: If you have hundreds of sequences with 'frag' features, you can edit this feature style once globally by selecting Options | Default Symbols with no sequences open. The selected style becomes the default for all new sequences with that feature from then on. This will avoid the necessity of making the same edit hundreds of times. Also, the initial settings for which default features are visible in a map can be set globally here.

Option 2. Globally change all 'frag' features to a supported feature type.

1. Open all the sequences at once by selecting them in the Finder and dragging them onto the MacVector application icon.

2. Select File | Save As... and select GCG-RSF as the export format.

3. Set the Window popup to All Open Sequences and then select Save. This saves all the sequences into a single file.

4. Open the resulting .rsf text file in a text editor, then perform a Search-and-Replace 'frag' with any other valid feature type.

Potential feature types include source, old_sequence, gene, insertion_seq, misc_feature, primer_bind, etc. In many text editors, all the changes can be made at once with a single mouse click.

5. Save the changes to disk.

6. Reopen the .rsf file in MacVector. All the sequences will open individually and can now be re-saved.

Thu May 05, 2011 1:55 pm
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