Engineering issues in annotation
What sequence to start with?
- Because features are intervals on a sequence, problems can be caused by gaps, frameshifts, and other changes to the sequence. How do you track these changes over time and model features that span gaps?
When to annotate?
- Feature identification can aid in sequencing. It may be advisable to carry out sequencing and annotation in parallel thus enabling them to complement one another.
What analyses need to be run and how?
- What dependencies are there between various analysis programs?
- What parameters settings to use?