One of our lab's goals is to make it possible to systematically search for homologs of RNAs in genomes, not just by looking for sequence conservation but also by looking for RNA secondary structure conservation. A powerful model framework for RNA structure/sequence comparison, called profile stochastic-context free grammars (profile …
In the latest version of the HMMER website we have focused on enhancing the recognition and display of domains and motifs found in query sequences. To achieve this we added two new features to the site, additional HMM databases and simple motif detection.
We have …
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.
Science is running a poll titled "The Well-Behaved Scientist" this week that asks "how should we promote publication of data that can be replicated and reproduced?" Of the ideas on their list -- more funding from funding agencies, more rewards from institutions -- conspicuous in its absence is the rather fundamental idea …
Most scientists get to have their research programs reviewed quietly behind closed doors. But if your upcoming contract review gets featured in Nature under a title "A roll of the dice", um, is that a good sign, or bad?
Janelia is accepting applications for our 2012 summer undergraduate research program, deadline January 13. Janelia pays all expenses, travel, and a stipend for the 10-week program here at the Farm.
The program is particularly terrific for students interested in systems neuroscience, since Janelia is a neurosciency place, but there's a …
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 …
We've had a couple of reports of some less-than-intuitive behavior of HMMER3 on poor-scoring sequences. As one correspondent described it, HMMER3 is stubborn. It will refuse to score and align certain low-scoring sequences no matter what options you try to set. It's probably worth explaining this behavior in public, partly …
Goran and our systems wizards will be upgrading Janelia's network and some of our filesystems over the holiday weekend. We expect web services hosted by our lab will be unavailable at least sporadically from Friday evening \~8pm through Sunday \~4pm. This includes hmmer.org and HMMER RESTful computing services, access …
I've written parts of HMMER's code in the shadow of a massive Tyrannosaurus, and this week I'll get to do it again. I'm on an advisory committee for the Field Museum of Natural History in Chicago, surely one of the few places you can sit in a cafe amongst dinosaurs …