By Matthew Dublin

Sean Eddy, a bioinformaticist at HHMI's Janelia Farm campus, is giving all HMMER users out there one to grow on in his latest post over at Cryptogenomicon. Eddy, HMMER's developer, says that since the release of HMMER3 the amount of emails from users he is constantly bombarded with is becoming unmanageable. Most of the emails are from people who are just not reading the darn documentation or disclaimers (you know who are). Because most of these HMMER inquiry emails seem to center around the three questions below, Eddy has listed the following responses/disclaimers, in an attempt to prevent both his inbox from over flowing as well as any hurt feelings you might have as a result of not getting a reply back because he can't possibly respond to every single email:

How do I do X in HMMER? If you ask me a question that’s already covered in HMMER3’s documentation, I may not reply, in the hope that you realize you can just do your homework. It’s a little awkward to get into a “please read the documentation”, “I did”, “no you didn’t; look at page XX” discussion with a lot of people during the day; partly because I tend to get more testy than I ought to be, partly because I tend to answer in a hurry and make embarrassing mistakes, and partly because it becomes faster to just answer the question rather than have that discussion, but I didn’t have time to answer the question in the first place. Of course, if someone finds something that I haven’t documented well, I always reply, and I always fix the documentation so I don’t have to reply to similar questions in the future. I’m much more likely to reply if someone indicates that they’ve already read the documentation carefully, rather than taking advantage of my easy email accessibility.

How do I do X in this interface to HMMER? If you’re using someone else’s software or web interface to use HMMER, and your problem is in their software not mine, your first point of contact should be the person who developed the interface. That includes commercial software packages that bundle HMMER, and things like BioPerl and other Bio* interfaces. I’m much more likely to reply if a question is directly about HMMER’s own input/output, not something that’s been filtered through someone else’s interface.

How do I do X in this thing that’s called *HMMER* but really isn’t? Programs like MPI-HMMER, GPU-HMMER, LD-HMMER and the like are using the name HMMER without our permission, in annoying disregard of my attempts to get them to use a name that doesn’t confuse people and burden me with a bunch of extra email. Except for the software released by us from hmmer.org, we don’t have anything to do with these other forks or clones, and you again need to contact the people responsible for them.