It has been a couple of weeks now since we released jackhmmer on the HMMER website and so far (touch wood etc…), it seems to be performing as we had hoped – here on ‘the farm’ we are getting very excited with the results we are observing. Continue reading →
Have you ever wondered how a new protein family would look in context of other Pfam domains? Well, look no further than the hmmer website! At the end of last week we released a new way of visualizing search results according to ‘domain architecture’ (applies to both phmmer and hmmsearch). Continue reading →
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.
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 and Jody Clements here in the skunkworks at HMMER Labs, HMMER searches are now available on interactive web servers.
Continue reading →
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”, is still in progress — a generative probabilistic interpretation of what all the explicit and implicit zero scores in Smith/Waterman scoring really “mean”, and the nonzero values we say they ought to have. Temple Smith has said his career was based on zero, referring to the extra step in the Smith/Waterman local alignment recursion compared to global sequence alignment. Sergi’s going to show that Temple’s career is and always should have been nonzero.
Diana Kolbe, one of our two last Washington University grad students, defended her thesis back in St. Louis yesterday. She’s worked for many (!) years on ways to accelerate the Infernal software for RNA similarity search. An important last chunk of her work, which we hope to write up for publication in addition to what’s in her thesis, established proof of principle for a structure-based heuristic acceleration that complements Infernal’s current sequence-based heuristic acceleration. It will take significant software engineering to implement her ideas in the production codebase, and she’s more than done her time in grad school already, so we’re letting her go; the proof of principle is captured in an Infernal development snapshot release. She’s off to join Laura Elnitski’s lab at NIH NHGRI as a postdoc.
The lab is getting close to completing a gradual four-year transition from its WashU configuration (where we were about 15 people, almost entirely built around me working with graduate students, and a sprinkling of postdocs and staff) to its Janelia configuration (where we are about 6 people, and the long-term plan is to have a core of staff working on software engineering in HMMER and Infernal, with me working on shiny new things with one or two postdocs). The last Washington University graduate student, Seolkyoung Jung, is now writing her thesis and her last paper; we’ve just submitted her magnum opus, a paper describing an enormous chunk of work on finding ncRNAs in Oxytricha trifallax.