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Gene prediction algorithm PRODIGAL

With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results… [Read More]

Naegleria genome project on Medical News Today

Scientists have now sequenced the genome of a weird, single-celled organism called Naegleria gruberi that is telling biologists about that transition from prokaryotes, which function just fine with all their proteins floating around in a soup, to eukaryotes, which neatly compartmentalize those proteins? The sequence, produced by the Department of Energy Joint Genome Institute (JGI),… [Read More]

Naegleria genome project on Daily Cal

This aspect of the organism could be particularly interesting to the medical field, according to Prochnik. Because the organism’s and human cells’ flagellate tails are exactly the same, the two can be related.  “When flagellates go wrong it causes problems like blindness, kidney diseases, obesity and developmental defects,” he said. “So the more we learn… [Read More]

Naegleria genome project on UC Newsroom

Scientists have now sequenced the genome of a weird, single-celled organism called Naegleria gruberi that is telling biologists about that transition from prokaryotes, which function just fine with all their proteins floating around in a soup, to eukaryotes, which neatly compartmentalize those proteins?  The sequence, produced by the Department of Energy Joint Genome Institute (JGI),… [Read More]

Naegleria genome project on KPCC Pasadena

“Naegleria‘s pretty amazing because it can make one of these structures entirely from scratch. And it does it really fast,” Fritz-Laylin says. “It can do it in an hour to an hour and a half.”  She wanted to understand how that happens. And sure enough, there are clues in the organism’s genes. She and her… [Read More]

Naegleria genome project on Boston’s WBUR

These days, when you want to see what makes an organism tick, you order up a scan of its genes. And as it happens, scientists at the Department of Energy’s Joint Genome Institute in Walnut Creek, Calif., were sequencing a bunch of organisms, and they had a little extra room in their DNA-reading machines. So… [Read More]

Naegleria genome project on Bay Area PBS (KQED)

Step aside, Dr. Jekyll and Mr. Hyde. Here’s a story about an organism that dramatically transforms itself when it’s under stress. It turns from a lethargic amoeba into a sprightly, two-armed swimmer. This unlikely single-celled creature is named Naegleria gruberi. It lives in the dirt, under the eucalyptus trees, on the University of California, Berkeley… [Read More]

Naegleria genome project on Bay Area’s ABC7 news

At UC Berkeley, there is new hope for some of mankind’s biggest maladies from research about the smallest of creatures.  “What we have found is fundamental,” Simon Prochnik, a bioinformaticist at the DOE Joint Genome Institute, said.  Prochnik studies the genetic make-up of single celled amoebas. He and a team of researchers have now sequenced… [Read More]

BNET on PacBio’s first customers

Last week, Pacific BioSciences, which claims it will map a genome in 15 minutes for less than $1000 by 2013, announced several new partnerships which they say will help customers “rapidly and easily adopt” their sequencing technology. That’s big news, because Pacific BioSciences’s customers are ten research institutions, including major players in genetics like The Broad Institute… [Read More]

Naegleria genome project on NPR

Step aside, Dr. Jekyll and Mr. Hyde. Here’s a story about an organism that dramatically transforms itself when it’s under stress. It turns from a lethargic amoeba into a sprightly, two-armed swimmer. This unlikely single-celled creature is named Naegleria gruberi. It lives in the dirt, under the eucalyptus trees, on the University of California, Berkeley… [Read More]