(Press-News.org) Sequencing the DNA of an organism, whether human, plant, or jellyfish, has become a straightforward task, but assembling the information gathered into something coherent remains a massive data challenge. Researchers using computational resources at the San Diego Supercomputer Center (SDSC) at the University of California, San Diego, have created a faster and more effective way to assemble genomic information, while increasing
In a paper presented the past month at the 39th International Conference on Very Large Databases (VLDB2013) in Riva del Garda, Italy, Xifeng Yan, the Venkatesh Narayanamurti Chair of Computer Science at the University of California, Santa Barbara, explains how he used SDSC's Trestles compute cluster to help develop a new algorithm called MSP (minimum substring partitioning) that helps to assemble genomes with extreme efficiency. MSP is a critical part of a pipeline, or a group of software that assembles entire genomes, with each piece of the software doing one part of the job. Yan and his colleagues were able to optimize one of two steps to use a mere 10 gigabytes of memory without runtime slowdown.
"High-quality genome sequencing is foundational to many critical biological and medical problems," said Yan. "With the advent of massively parallel DNA sequencing technologies how to manage and process the big sequence data has become an important issue. Experimental results showed that MSP can not only successfully complete the tasks on very large datasets within a small amount of memory, but also achieve better performance than existing state-of-the-art algorithms."
According to Yan, his experimental results demonstrate that MSP's improvement in efficiency might soon make it possible to assemble large genomes using smaller, less expensive, commodity clusters rather than requiring high-cost, high performance resources.
Knowing the whole genome of various species underlies biological and medical research, such as understanding evolution pathways or identifying the cause of diseases. However, existing sequencing techniques produce huge amounts – billions for a higher organism such as a human – of overlapping short sequence randomly sampled from the genome. A major challenge in genome research is to assemble those short reads, which vary from ten to several hundred bases, back into the whole genome, a task that requires vast amounts of memory. It would be similar to gluing together an encyclopedia from a haystack of words and sentence fragments.
Using Trestles, Yan and his colleagues demonstrated that MSP reduces one of the steps required so that it uses significantly less memory than widely-used algorithms, removing one of the bottlenecks in processing whole genomes. Algorithms such as Velvet and SOAPdenovo struggle to computationally to prepare a virtual scaffolding upon which to assemble the sequence into complete genomes. MSP, a disk-based partition method, streamlines the creation of such scaffolding, known as a De Bruijn graph. A mammalian-sized genome processed using other algorithms would consume hundreds of gigabytes of memory, while MSP allows researchers to complete a key step to ten gigabytes of memory without runtime slowdown.
Yan and his colleagues are working on a second step that also consumes a significant amount of memory, and have so far reduced its memory use by two-thirds with the goals of further reductions in the future. Additional researchers include Yang Li, Pegah Kamousi, Fangqiu Han, Shengqi Yang, and Subhash Suri, all with UC Santa Barbara. The full paper can be viewed at http://www.cs.ucsb.edu/~xyan/papers/vldb13_debruijn.pdf.
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PROVIDENCE, R.I. [Brown University] — To stay ahead in the race against drug-resistant infections, scientists constantly search for and exploit vulnerabilities in deadly bacteria. Now, researchers from Brown and the Massachusetts Institute of Technology have used a novel compound to exploit an Achilles' heel in the bacterium that causes tuberculosis.
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A team of researchers supported by the Clemson University Experiment Station, Extension Service ...
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Findings were based on a Hass Avocado ...
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Typical drug delivery systems act more like sponges than bottles. For example, drugs are absorbed into polymer particles and then allowed to diffuse out over time. The researchers hope that the new system may allow for greater control of drug delivery. Cargo would stay inside the hollow polymer particle when plugged with a solid cork. When the cork is melted by ...
(Santa Barbara, Calif.) –– The female common market squid –– AKA Doryteuthis opalescens –– may not be so common after all. Researchers at UC Santa Barbara have discovered that this glamorous cephalopod possesses a pair of stripes that can sparkle with rainbow iridescence. These flank a single stripe, which can go from complete transparency to bright white.
This marks the first time that switchable white cells based on reflectins –– the proteins responsible for reflecting light as color –– have been observed. The findings are published in the Journal of Experimental Biology.
The ...
By analyzing the distinctive cracks lining the icy face of Europa, NASA scientists found evidence that this moon of Jupiter likely spun around a tilted axis at some point.
This tilt could influence calculations of how much of Europa's history is recorded in its frozen shell, how much heat is generated by tides in its ocean, and even how long the ocean has been liquid.
"One of the mysteries of Europa is why the orientations of the long, straight cracks called lineaments have changed over time. It turns out that a small tilt, or obliquity, in the spin axis, sometime in ...
BLOOMINGTON, Ind. -- Pioneering new research from a team of Indiana University Bloomington biologists has shown for the first time that a protein which has been long known to be critical for the initiation of protein synthesis in all organisms can also play a role in the regulation of gene expression in some bacteria, and probably land plants as well.
The protein, called translation initiation factor 3, or IF3, is one of three proteins that make up the core structure of the machinery needed to guide the joining of messenger RNAs and ribosomes as protein translation commences. ...
As e-readers grow in popularity as convenient alternatives to traditional books, researchers at the Smithsonian have found that convenience may not be their only benefit. The team discovered that when e-readers are set up to display only a few words per line, some people with dyslexia can read more easily, quickly and with greater comprehension. Their findings are published in the Sept. 18 issue of the journal PLOS ONE.
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