Infernal 1.0

Infernal logo

Infernal 1.0 — the first production release of our software for RNA sequence/structure homology search and alignment — has been released. Source code and documentation are available over at

Infernal development is now led by Eric Nawrocki in the lab.

Infernal’s actually been used by the Rfam database since about 2002, in pre-1.0 versions. This is the first version that we think is really ready for production use, more than just a testbed for algorithms. The 1.0 code went through several release candidates in the past few months. We think we have all the obvious bugs shaken out of it.

The problem Infernal addresses is RNA homology search. Continue reading →

HMMER3 alpha test release

I have one concluding favor, to request of my Reader; that he will not expect to be equally diverted and informed by every Line, or every Page of this Discourse, but give some Allowance to the Author’s Spleen, and short Fits or Intervals of Dullness…

Jonathan Swift, A Tale of the Tub

HMMER3 alpha test code is now available as a tarball at our FTP site. Later this evening, it’ll also be linked from the HMMER web page.

It includes a User Guide with introductory notes about installation and tutorial examples of command line usage. The guide is telegraphic, documenting basic usage of the new HMMER3 programs. It does not yet go into all the command line options — partly because a few of them don’t work as advertised yet.

Linux binaries are included, as well as source code. If you compile it for yourself, be aware that you need a compiler that deals well with Intel Streaming SIMD Extensions (SSE), specifically SSE2 code. The GNU C compiler gcc will compile HMMER fine, but it produces binaries with markedly suboptimal speed performance. We now use the Intel C compiler, icc, for production code. The Linux binaries in the tarball have been compiled with icc.

The purpose of the alpha test period is in part to smoke out any remaining bugs, of course, but also to give people a chance to give feedback on how it all behaves at the command line. The core of H3’s functionality seems stable to me, but all the stuff that you see — the applications, the command line options, the i/o formats — is deliberately still protoypical and fluid. The invited alpha testers are a group of power users at centers that do high throughput annotation. In the test phase, I’d like to be free to make changes that make HMMER3 work best in anyone’s analysis pipeline. The corollary to this is that you can’t count on HMMER3 output formats just yet, so don’t go writing any heavy duty parsers.

There are eleven “invited” alpha testers, but anyone else adventurous enough to test the code is welcome to. The code is publicly accessible. The best place to leave comments and discuss issues/problems/bugs is here at Cryptogenomicon.


And how will it ever end?
unless the day finally arrives
when we have compared everything
in the world
to everything else in the world,

and there is nothing left to do
but quietly close our notebooks
and sit with our hands folded on our desks.

– Billy Collins, The Trouble With Poetry

Ryan Richt pointed out in a comment, so what if HMMER3 is as fast as BLAST; even BLAST isn’t fast enough these days!

That’s an interesting comment. I think we’ve reached a turning point in the field. I think we will now see a schism between tools that do remote homology search, versus tools that do rapid mapping of reads to identical or near-identical reference genomes. We’ve used BLAST as our jack-of-all-trades for over a decade. It’s the lineal descendant of the first dynamic programming sequence alignment routines that were happy just to score alignments by percentage identity. Modern needs are now pressing it on two very different fronts. Continue reading →

HMMER3 alpha test release: Monday January 12

HMMER3 is spawning a lot of work. It may never be “done” to my satisfaction. It might be that the best way forward is to release it and get it onto an evolutionary trajectory. So this’ll be an odd “alpha test”. A lot of the functionality that I plan to put in HMMER3 isn’t there. But, ready or not, barring some last minute glitch, I’m releasing the first alpha test Monday. Continue reading →