How to automatically annotate bare sequences

If you have an unannotated vector or other sequence that you’ve been sent from a sequencing lab, downloaded from a web page or been sent by a colleague, it can be very tedious to manually create all the features that you believe are present on the sequence – assuming you even know what is supposed to be there! Luckily, there is a simple solution in MacVector: Open the sequence (or create a new Nucleic Acid Sequence document and paste in the residues), make sure you have the Topology set correctly to either circular or linear, then choose Database | Auto-annotate Sequence.


The main key to this functionality is to select a suitable Sequence Folder to scan, as circled in the screenshot. A good place to start when trying this out for the first time is the /Applications/MacVector/Common Vectors/ folder. We have collected a selection of common vectors from a variety of manufacturers, made sure they are correctly annotated and given each feature a unique and attractive graphical appearance.

After clicking OK, MacVector will scan through the entire hierarchy of folders in Common Vectors, opening each sequence, extracting the features and determining, via sequence similarity, if the same feature is present in your starting sequence. When complete, a dialog will appear listing the number of features analyzed and how many were found on your sequence. MacVector is clever enough to know not to count duplicate features, and also to allow a little “fuzziness” in the similarity calculation.

Of course, this will only find features common to these cloning vectors – repeat the search with a folder full of your own annotated sequences to find those. Then, if there are still features missing, manually add those. This way, you can slowly build up your own collection of curated sequences to act as a “database” for rapid annotation of any new sequences you acquire.

There is a longer blog post and a tutorial installed on your computer at:

/Applications/MacVector/Documentation/Auto Annotation Tutorial.pdf

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