Thanks to everyone who provided comments and suggestions for my talk for NIH NHGRI's five-year planning process meeting on The Future of the Large-Scale Sequencing Program, March 23-24 in Bethesda. A copy of my slides is here, if you're interested.

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 …

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 …

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 …

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 …

A commenter asked yesterday about support for Sun SPARC VIS instructions in HMMER3, and I accidentally deleted the comment in an enthusiastic burst of spam-purging. Have now upgraded WordPress and turned on the akismet spam filter; will see if that helps.

Anyway, in penance for my poor comment moderation: a …

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.janelia.org.

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

Infernal's actually been used by the Rfam …

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 …

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 …

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 …