General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Controlling The Automatic ORF Display in MacVector 15.5

MacVector automatically scans every DNA sequence window for open reading frames and displays the results in the Map tab.

NewImage

The setting for this are controlled by the MacVector | Preferences -> DNA Map pane, along with the automatic Show restriction sites settings.

NewImage

The Minimum Number of Codons setting is fairly obvious. 5’ ends are starts and 3’ ends are stops are used for linear sequences and will display ORFs coming into the sequence that do not have a start codon, or ORFs that read out of the sequence without a stop codon. Codons after stops are starts is useful if you just want to know the locations of the longest possible ORFs in a sequence, irrespective of the existence of a start codon. Finally, the Suppress annotated CDS ORFs check box prevents the display of ORFs that are already annotated. However, if a potentially longer ORF is present, e.g. there is another ATG codon upstream, that ORF will be displayed. You can read more details here.

The appearance of the ORFs can be controlled using the Options | Default Symbols menu item.

This entry was posted in Tips and tagged , , , . Bookmark the permalink. Trackbacks are closed, but you can post a comment.

Post a Comment

Your email is never published nor shared. Required fields are marked *

You may use these HTML tags and attributes <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <s> <strike> <strong>

*
*