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A new breakthrough software system, designed by Ryan Tarpine GS, is allowing biologists to find their way through the genomic DNA sequence. The program, called the CYRENE cisGRN Browser, determines the regions of new genomes that scientists do not understand well or do not know yet.

The Browser is "like a GPS Google Earth map of the regulatory genome," Sorin Istrail, director of the Center for Computational Molecular Biology and professor of computer science, who collaborated with Tarpine on the program, wrote in an e-mail to The Herald.
The program looks at millions of pieces of DNA sequence of a species and pinpoints their location in the genome of a related species by finding where the DNA pieces match, wrote Tarpine, a doctoral candidate in computer science.

For example, experimenting on two species of sea urchins that share a common ancestor, the program attempts to find "for each piece, whether four or fewer mutations occurred during its evolution as the two species developed. If, during millions of years of evolution, four or fewer mutations occurred, then that piece is most likely part of sequence that has a function," Tarpine wrote.

By analyzing the experiment's final results, biologists can then focus on areas of functions and regions of new genomes they do not understand well, Tarpine wrote.

Sequencing the genome of a new species is expensive and requires a lot of time, Tarpine wrote, and new technologies such as "high-throughput sequencing" — while not costly and able to quickly produce some of the DNA sequence of a genome — only give a small amount of DNA pieces.

The new software program is significant in "utilizing these inexpensive technologies in combination with the whole genomes already known," Tarpine wrote.

The result of three years of collaboration and research, the software program was operated in the lab of Eric Davidson, a world-renowned experimental biologist and current professor of cell biology at the California Institute of Technology, Istrail wrote.

Biologists at the lab have been using Tarpine's Browser, which serves as an analytical instrument, to conduct wet-lab experiments, Istrail wrote.

The National Science Foundation funded the program and all its research, he wrote.
Istrail also wrote that the combined effort of both Brown and Caltech would increase the speed of scientific discoveries.

"It used to be ... five years of research was needed to reveal the circuitry of one cis-module gene's regulatory region. Now we can do in a few months 100 cis-modules of 50 genes," Istrail wrote.

Tarpine wrote he agreed on the importance of increasing the program's speed in the future.
"I will always be trying to make it faster," he wrote.


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