You can use the Database->Auto-Annotate Sequence function to quickly annotate a bare sequence using existing annotated sequences on your file system. However, this only works if your collection of sequences contains features representing all parts of the bare sequence. Luckily, if you have an unannotated region after running Auto-Annotate, you can use MacVector’s built-in BLAST function to find and download matching annotated sequences, then run Auto-Annotate to add features to the blank region.
If you are interested in this, the full steps are discussed in this blog article.