In preparation for running some investigations beyond annotation this coming semester, we've been working though the suggestions in the 2013 "Exploring bacteriphage biology" document found on phagesdb, and we've been working through softberry to find terminators. We'd like to write up a "protocol" for our undergrads, but we're having a hard time finding info on how to interpret the data. Who else has used this program, and can you point us to pre-written protocols/resources? Most papers we found don't explain how they used it at all.