Peter Lawrence and Michael Locke wrote an essay that made an enormous impression on me ("A Man for Our Season", Nature, 1997). For a long time a copy hung on the wall of the lab. I was reminded of it last week when I read a recent interview with Lawrence …
Over at our publications page, I've posted a preprint of Elena Rivas' latest paper on RNA secondary structure prediction, which she submitted for review today.
The state of the art in RNA secondary structure prediction is arguably starting to move towards statistical models, instead of (or in addition to) thermodynamic …
From today's email...
Suppose, for example, you want to search 300 million metagenomic sequence reads, each about 200nt long, against the Pfam database. What's the best way to do that task with HMMER3? The bottom line: use hmmsearch, not hmmscan. For the numerology of why (and chapter and verse on …
The HMMER and Infernal code includes some hidden tools: the Easel library, and its "miniapplications". Easel is our code library (in the easelsubdirectory of both HMMER and Infernal), and the miniapplications (in easel/miniapps) are a set of command line utilities that we use for manipulating sequence data. For …
Over at hmmer.janelia.org, you'll notice a significant change over on the right side of the page. See the "Search" button? You don't have to use HMMER at the UNIX command line any more. Thanks to support from the Howard Hughes Medical Institute, and hard work from Rob Finn …
I've added some sections to the version of the HMMER User's Guide that's linked at hmmer.org. You can download the new Guide from here.
The Guide now briefly describes the HMMER3 acceleration pipeline for profile/sequence comparison, and the methods used to identify domain "envelopes", maximum expected accuracy alignments …
Human language is a cracked kettle on which we beat out tunes for bears to dance to, when all the time we are longing to move the stars to pity.
Gustave Flaubert, Madame Bovary
I regret to announce the untimely death Monday morning of Michael Farrar, principal software engineer for …
The Xfam team in Cambridge is advertising an open curator position. Join the Xfam team, see the world! At least some of the best parts of it: Cambridge UK, Stockholm Sweden, and our beautiful, secluded, mysterious Janelia Farm on the banks of the Potomac River near Washington DC.
The National Academy of Sciences has just released the report Sequence-Based Classification of Select Agents: A Brighter Line. A committee of 13 of us, chaired by Jim LeDuc (Director, Galveston National Laboratory, University of Texas Medical Branch) and cat-herded by India Hook-Barnard (NAS), has been working on this report for …
Our little Janelia lab got even smaller this week.
Sergi Castellano left to take a new faculty position in the Department of Evolutionary Genetics with Svante Paabo at the Max Planck in Leipzig, Germany. Sergi's postdoctoral work on single-sequence-query homology searches in HMMER, the project we call "Smith/Waterman: reloaded …