Scientists’ effort to piece together the genome is taking a significant step forward with a new computerized method that creates more complete and detailed versions of the complex puzzle of life than have ever been produced before.
“We hope and expect this advance will change how new genomes will be sequenced and studied since it gives such an improved view of what is really there,” said Michael Schatz, Bloomberg Distinguished Associate Professor of computer science and biology within Johns Hopkins University’s Whiting School of Engineering and Krieger School of Arts and Sciences. Schatz coordinated a group of 17 scientists from nine institutions in publishing their results in the current issue of Nature Methods.
“Without this approach, you will simply miss a lot of important gene sequences, and many errors can be introduced,” said Schatz, who worked closely with researchers at Pacific Biosciences in Menlo Park, California, and Cold Spring Harbor Laboratory in Cold Spring Harbor, New York. He was joined by Johns Hopkins colleague Fritz J. Sedlazeck, a postdoctoral researcher.
Also involved in the research were scientists from the U.S. Department of Energy Joint Genome Institute; the Salk Institute for Biological Studies; University of California, Davis; University of Nevada, Reno; Universita degli Studi di Verona, Verona, Italy.
The development of the two algorithms, FALCON and FALCON-Unzip (which are available free to the public), Schatz said, is analogous to the move from a primitive telescope “that can only see the closest, brightest objects in the sky, to the Hubble space telescope that can dramatically improve the resolution to see things that are much more distant and in much greater focus.”
The improvement from previous methods could have a significant impact in biology and medicine, as “genome assembly is one of the most fundamental and important steps in molecular biology to study the genetics of any living thing,” he said.
Another group of scientists has already used versions of the software to assemble and study the gorilla genome earlier this year, and Schatz said his lab is using the method to study plants, animals, and microorganisms that cause disease as well as healthy and diseased human genomes, including studies of cancer.