HMMER 3.0rc2: HMMER3’s release candidate 2

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In a world where “a few days” means a month; in a world where “HMMER3 is ready” means another release candidate: ta-da! A release candidate!

HMMER3 release candidate two is available for download as a source code tarball. Over at hmmer.org, there are also links for downloading tarballs including precompiled binaries for Linux/Intel ia32, Linux/Intel x86_64, and Mac OS/X Intel platforms.

The release notes for 3.0rc2 follow:
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bug #h77: hmmalign corrupts column before an all-delete column

Denis Schmidt (University of Frankfurt) has reported a critical bug against hmmalign in 3.0rc1.

Any time there is an alignment column consisting of all deletions, the code is supposed to remove the alignment column altogether; instead, it overwrites the previous alignment column with an all-delete column, which most likely overwrites sequence residues and corrupts the alignment.

I inadvertently introduced this bug in 3.0rc1, when fixing a different issue. 3.0b3 does not have the bug.

A workaround is to use ‘hmmalign --allcol‘. The --allcol option makes every column appear in multiple alignments, even if it consists entirely of gap characters (i.e. a consensus position that none of the aligned sequences have a residue for).

The bug is fixed in the 3.0 release branch code, and the fix will appear shortly in the next release.

HMMER 3.0rc1: HMMER3’s release candidate 1

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After a year of alpha and beta testing, HMMER3 is ready. Release candidate 1 is available for download as a tarball. It includes precompiled binaries for Intel/Linux systems, both 64-bit (x86_84) and 32-bit (ia32) platforms, and you may just copy these into some directory in your $PATH if you like. If the precompiled versions don’t work for you, you can always compile your own version from the source.

Of course, “ready” is a euphemism for the balance of terror between the community complaining that Pfam (and Interpro, and more) are running on our beta test code, versus our never-ending to-do list of things we want H3 to do. We’re at a stable release point, but we also have a lot left on our to-do lists.

Assuming we don’t find anything more than a few typos in 3.0rc1, we’ll upgrade to a full 3.0 release in a few days.

The release notes for 3.0rc1 follow:
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HMMER 3.0b3: the final beta test release

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The final HMMER3 beta test release is available for download as a tarball. It includes precompiled binaries for Intel/Linux systems, both 64-bit (x86_84) and 32-bit (ia32) platforms, and you may just copy these into some directory in your $PATH if you like. If the precompiled versions don’t work for you, you can always compile your own version from the source.

The main additions in 3.0b3 are parallelizations and even more speed. It now includes support for multicores (POSIX multithreading) and support for clusters (MPI). For the first time, we’re seeing some searches peek above NCBI BLAST search speed. Yes, you read that right, profile HMM speeds have started to exceed BLAST speed. And we’re far from done.

The release notes for 3.0b3 follow: Continue reading →

Summary of known bugs (so far) in 3.0b2


The truth will set you free. But not until it is finished with you.

— David Foster Wallace, Infinite Jest

With the release of Pfam 24, HMMER3 beta test code has been pressed into service just a bit earlier than we’re comfortable with. Though the 3.0b2 code seems to be holding up reasonably well, we are aware of six bugs — two in how H3 handles Pfam GA/NC/TC cutoffs, two in how H3 handles the ‘*’ nonresidue character that some sequence files use to represent stop codons in translated DNA, one in hmmscan’s tabular domain output (“domtbl”) format, and one in sequence description lines with % characters causing crashes in jackhmmer. All six are fixed in the development trunk. We are starting our test/release cycle for 3.0b3 (the third and probably final beta release) now. The fixes will be included in 3.0b3, along with some important new functionality I’ll discuss on the blog soon.

More details on the six bugs are below the fold.
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Radio silence: ended


Writing and drawing are slow, deliberate activities, so I tried to keep distractions to an absolute minimum, and I did everything myself. I liked this control, as it fostered a sense of craftsmanship. There was great personal satisfaction in attending to detail and quality, and I remain very proud of the standards the strip met day after day. I also liked the responsibility of knowing that, succeed or fail, it was all my own doing.

— Bill Watterson, Calvin and Hobbes

Besides writing code all day, one of the more interesting things about the job is what I get to do on the side. Technically, Janelia expects me to be physically present for nine months a year, and it gives me three months to do whatever I want — skiing in New Zealand, NIH study section, visiting some university and giving a seminar, swine flu, it all counts against my three months of “vacation time” as far as Janelia’s concerned. So. Mild-mannered software/bio geek by day; advisor to US government agencies by… uh, well… seemed like pretty much the whole summer, this year. Two big time commitments with serious committee reports to help write. One report is finished for the Department of Defense, and another is well underway for the National Academy of Sciences. That, plus three weeks in Spain for the Benasque RNA conference, plus some review work for NIH all pretty much enforced a personal vacation away from the HMMER code. Probably good, because the code was making me cross-eyed, not to mention cross. I needed a break from it.

Nonetheless, despite a few months of radio silence, things have been moving forward for HMMER3. Especially on the Grand Long Term Strategy front. HMMER now has a development team.

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