Biological 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 co-organizers. Janelia Farm conferences are small (~50 people), a nice size for conversation and thought. We’re likely to select about 15 more participants from open registration. For more information, including a current list of the invited speakers and a link to registration, see the Janelia conferences web page.

ENCODE 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, and Jerzy Jurka just released a new data resource that annotates nearly 50% of the human genome as transposable element-derived, and transposon-derived repetitive sequence is the poster child for what we colloquially call “junk DNA”.

The newspapers went on to say that ENCODE has revolutionized our understanding of noncoding DNA by showing that far from being junk, noncoding DNA contains lots of genetic regulatory switches. Well, that’s also odd, because another part of my lab is (like a lot of other labs in biology these days) studying the regulation of genes in a model animal’s brain (the fruit fly Drosophila). We and everyone else in biology have known for fifty years that genes are controlled by regulatory elements in noncoding DNA. (Well, I’ve only known for thirty years, not fifty, I admit — only since Mrs. Dell’Antonio kicked me out of high school biology class and gave me a molecular genetics textbook to read by myself.)

Now, with all respect to my journalist friends, I’ve learned not to believe everything I read in the newspapers. I figured I’d better read the actual ENCODE papers. This is going to take a while. I’ve only read the main Nature paper carefully so far (there’s 30+ of them, apparently, across multiple journals). But it’s already clear that at least the main ENCODE paper doesn’t say anything like what the newspapers say.

The ENCODE project and our existing knowledge of genomes are both vastly more substantial than the discussion the ENCODE authors are provoking in the press right now.
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Dfam: 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 using searches with single sequence consensuses to using searches with profile HMMs, now that the HMMER3 project has made DNA/DNA profile HMM searches sufficiently fast for whole genomes. Dfam is a collaboration between Jerzy Jurka and his Repbase resources (Genetic Information Research Institute), Arian Smit and his RepeatMasker software (Institute for Systems Biology, Seattle), the HMMER3 development team at Janelia Farm (particularly Travis Wheeler, leading nhmmer development), and the Xfam database consortium (particularly Rob Finn, here at Janelia). Among other effects of this work, we expect the widely used RepeatMasker software to include nhmmer, Dfam models, and profile HMM searches in the near future. A preprint of the first Dfam paper is available now on our preprint server, and the database itself is available for use at
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