Using HMMER2 models with HMMER3: don’t do that.

Thanks to our panopticon-like ability to scan the Internets for people benchmarking the HMMER3 alpha release even though we told you not to, it’s come to the attention of our Watchers that people are doing benchmarks using existing HMMER2 files (Pfam, SMART), taking advantage of HMMER3’s ability to read or convert HMMER2 format profile HMM files. There is something important you need to know, if you’re doing this. Continue reading →

HMMER 3 alpha test 2 release (3.0a2)


A new version of the HMMER3 alpha test code is available as a tarball available for download on our FTP site. Besides the source code, a binaries/ subdirectory contains precompiled binaries for Intel/Linux systems, both 64-bit (in binaries/intel-linux-x86_64) and 32-bit (in binaries/intel-linux-ia32), and you can just copy these into some directory in your PATH if you like. (That’s all a “make install” is going to do at the moment anyway.)

The release notes for 3.0a2: Continue reading →

Computational challenges in the future of large-scale sequencing


I’m preparing a plenary talk on Computational Challenges in the Future of Large-Scale Sequencing that I’ll give at a workshop on The Future of the Large-Scale Sequencing Program, which the NIH National Human Genome Research Institute (NHGRI) is convening in two weeks (Bethesda, 23-24 March 2009). This is part of a long range planning process for NHGRI. This will be the one talk at the workshop that focuses on computational biology’s future needs, so I’m aiming to present a community consensus view as guidance to NHGRI, not just my own view.

What do you think NHGRI should hear?
Continue reading →


MANAGER: Don’t wait because your piece is still in pieces! Whatever you’ve concocted is sure to be a hit, and simple recipes are simple to serve up. Nor does it help to offer anything complete — your audience will only tear it apart.

POET: You don’t appreciate how low such hackwork is, or how unworthy of a genuine artist. I see that you derive your principles from the fine efforts of incompetents.

MANAGER: Your accusation doesn’t hurt my feelings; a man who wants to be effective must know the worth of proper tools.

— Goethe, Faust

I suppose one advantage of a blog is that I can answer a lot of email questions in one fell swoop.

When will HMMER3 be publicly released? The plan is for the alpha test phase to last another month or so; beta test to take another couple of months; and a 3.0 release in the summer. That’s our story, and we’re sticking to it until September.

Can I use HMMER3 in a publication now, while it’s still in a test version? Sure. But if you write a paper criticizing some obscure aspect of H3 performance that I’ve overlooked, rather than first giving me useful feedback on a freely available pre-publication test I’ve made available to you out of the open and boundless goodness of my heart, um, well, don’t expect me to buy you any beers next time I see you.

When’s the next test version (alpha2) coming? Depending on whether you ask the Marketing Promises division of the lab, or the Coding Reality division, that answer is either a) February 12; or b) Real Soon Now. See first question.