An Inherent Problem with Annotation
With the constant influx of new software tools, new genomes, and new publications, the way we annotate genomes is always changing. We always know a bit more than we did last year, and often a lot more than we did 5 years ago.
This leads to an inherent problem, however, in that we only officially train SEA-PHAGES faculty once, and obviously Cohorts 1-8 were trained more than one year ago. In addition, the genome you worked on at the Bioinformatics Workshop may be nothing like the genome you're currently annotating, and you'll inevitably come across new and puzzling regions.
Before? No...After? No...During!
The question is, how can we share what we've learned with the whole SEA in a manner that helps you do the most up-to-date annotations possible? We can put out "What's New?" documents before you begin annotating, which we do, but these often only cover broad strokes rather than details. Or we can provide feedback after you've submitted your final annotation, which we also do, but these details can be easily forgotten over the summer before you tuck into your next genome, and may not apply if you have a different cluster phage anyway.
Therefore, to our mind, the best time to get feedback is while you're actively annotating your genomes. And while we love answering questions about the cool and interesting things you're finding, we'd like that answer to be shared with everyone who might be coming across something similar so we don't end up have to answer it many times over!
Which obviously brings us to the seaphages.org Annotation Forum, where we can give specific, real-time feedback in a manner that's visible to others who might have similar questions. Therefore, we strongly encourage you to use the forum for questions you've come across while annotating.
Reorganization of the Forum
Which brings me to the point: I've slightly rearranged the Annotation Forum and renamed/clarified/broken up some of the existing threads to try to make everything more transparent and useful. Within the main annotation forum, there are now specific sub-forums for questions about calling start sites, calling functions, getting the notes right, and more. Please go ahead and ask questions in any of these. Here are a few quick pointers...
- Post specific titles to your questions, like "Large gap in a Cluster F1 phage" or "Write NKF or leave blank in minimal notes?" This will help others find answers more than titles like "Question about two genes".
- On each thread, try to keep the discussion specific to that topic. So if someone asks a question about the difference between a hydrolase and an esterase, don't use that same thread to ask about the HHPred cutoff for a hydrolase. Instead, create a new topic.
- The Annotation Forums are public, which means students can use them as well. And their PhagesDB logins will also work on seaphages.org.