jrr-cpt

Would addition of support for promoter features require a relationship to a gene or transcript? We are unlikely to have that data in many cases. However, for some well-studied phages,...

The SO term for [promoter](http://www.sequenceontology.org/browser/current_release/term/SO:0000167) would be the level we need. Some phage genes use a host prokaryotic promoter, and others a phage RNA pol promoter. These can occur in...

IF we were to want to annotate transcipts as feature types, likely we would use [transcript](http://www.sequenceontology.org/browser/current_release/term/SO:0000673) and some of its children, like [polycistronic transcript](http://www.sequenceontology.org/browser/current_release/term/SO:0000078)

Jobs identical in all parameters but the scoring_model (using skewnormal) do not yield probabilities greater than 1. Given that we are analyzing two proteins, the evcomplex algorithm seemed the appropriate...

@cmungall This came up in the multiorganism working group. It is also relevant for a couple phage GO-CAM/Noctua models @sandyl27 and I are building. Can we have a set of...

As per latest multi-organism working group meeting, we should provide the list of desired proteins as a GPI (preferred) file until the load of all Swiss-Prot entries occurs. Under gene-ontology/go-site/metadata/datasets/...

I was thinking about this today in the context of single-step processes. Some virions are enveloped by budding internal to the cell, or by budding through a host membrane into...

It's good for the process terms to cover the most annotated processes. There are also some cellular component terms that would expand the ribbon in a useful way. I'm not...

@bgruening this is for the phage Galaxy instance and paper we hope to submit soon