Cryptogenomicon

Our quest is at an end.

– Monty Python and the Holy Grail

Four years in development, and a year in testing: HMMER3 has reached its first public production release. Do we have time for a beer and a small celebration before we write the manuscripts and move straight on to 3.1 development? No? Thought not.

HMMER3 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 3.0 follow:
Read more »

My relationship with email is fraught. On the one hand, it ravages my time and concentration; on the other hand, it’s better than the damned phone.
Read more »

The czar of Rfam in Cambridge UK, Paul Gardner, is advertising for a new co-czar. Jennifer Daub is off to New Zealand, which is great for Jen, but what will Rfam do without her? It’s a great opportunity to bring more order to the world of noncoding RNAs, for someone with interest and skill at the interface of bioinformatics and RNA biology. The officialese of the job posting is available at the Sanger Institute web site.

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:
Read more »

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.