We’ve talked in previous tips about annotating open reading frames as CDS features. However, what if your sequence has no annotated ORF? MacVector’s ANALYZE | OPEN READING FRAMES… tool will help you find any quickly.
However, if you are new to this tool there are a few options that may prove initially confusing. These options modify how ORFs are detected. They are intended to help you find ORFs when you may only have a partial fragment of a gene. So if you’ve just ran an ORF analysis and find too many CDS regions or if you cannot find an ORF and you are not confident you have the full gene, then remember this email!
In the two screenshots below we have a sequence with a single long CDS region (in blue). If we have these two options turned on then you will see three ORFS on the three forward frames (top image). If you turn them off you see a single CDS (bottom image).
Don’t forget to annotate your CDS region when you’ve found it. Many tools in MacVector will show additional information about a coding region if it is annotated as a CDS region. If you simply drag the ORF from the RESULTS window it will automatically annotated that as a CDS region. It will also include the coding region’s translation directly in the annotation.