The well-behaved journal
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...
View ArticleInteractive, iterative searches using jackhmmer
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...
View ArticleMore domains and motifs
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...
View ArticleInfernal 1.1: RNA alignment and database search, 10,000x faster
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...
View ArticleDfam: annotation of transposable elements with profile HMMs
We’re happy to announce the release of Dfam 1.0, a set of profile HMMs for genomic DNA annotation of transposable elements. This essentially constitutes an upgrade of repeat element annotation from...
View ArticleENCODE says what?
So I read in the newspaper this week that the ENCODE project has disproven the idea of junk DNA. I sure wish I’d gotten the memo, because this week a collaboration of labs led by myself, Arian Smit,...
View ArticleSt. Louis
A friend just sent this wonderful video of my favorite city, to make me wistful. We still get our coffee shipped from Kaldi’s, our old neighborhood coffee shop. The saying in the lab was “St. Louis:...
View ArticleBiological sequence analysis and probabilistic models: 24-27 March 2013
Registration is open for a conference on “Biological sequence analysis and probabilistic models”, 24-27 March 2013, here at Janelia Farm. Katie Pollard (UCSF), Adam Siepel (Cornell), and I are the...
View ArticleCongratulations Dr. Eddy
I’ve always been jealous of the Eisen brothers. Finally, some parity. Congratulations to my brother Nicholas who passed his PhD defense in synthetic organic chemistry at University of Connecticut...
View ArticleJoin Rob’s HMMER team
Rob Finn’s HMMER web services team is expanding. We’re looking for people to apply to two new positions to help Rob and Jody push forward on some important ideas for our services. We’re pushing in the...
View ArticleHMMER3.1 beta test 1 released
The HMMER dev team is happy to announce an upgrade release of HMMER3, release 3.1. A beta test version of the code is publicly available as a tarball available for download, or from hmmer.org, where...
View ArticleOpen position: Director, Advanced Computation and Technology group
Janelia has a scientific director-level position open in our computation and technology group: “The Janelia Farm Research Campus of the Howard Hughes Medical Institute seeks an exceptional individual...
View ArticleThis site has moved, to cryptogenomicon.org
I’ve migrated cryptogenomicon.org off to a commercial (wordpress.com) host. If you’re seeing this post, you’ve linked directly to the old blog site, rather than the current cryptogenomicon.org site,...
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