New Technique Speeds up Gene Expression Analysis

Numerical analysis method delivers more accurate results in a fraction of the time required for previous methods.

Scientists at Carnegie Mellon and the University of Maryland have discovered a new technique for estimating gene activity from RNA sequencing data. The new method, which they call Sailfish, can reduce a gene expression study that once took many hours to a few minutes.
Scientists have come to rely on repositories of RNA sequencing data from previous studies for new research studies, using supercomputers to re-analyze the data using new hypotheses. The conventional technique for analyzing RNA sequencing data requires the scientist to map short sequences of RNA (called "reads") back to their original positions in the larger molecule. The Sailfish method eliminates (or re-imagines) this mapping process by sorting and assigning the reads in advance to different types of RNA molecules. According to Carl Kingsford, associate professor at Carnegie Mellon's Lane Center for Computational Biology, "This numerical approach might not be as intuitive as a map to a biologist, but it makes perfect sense to a computer scientist."
The research team reports that the Sailfish method can complete an RNA analysis 20-30 times faster than conventional methods. They also say Sailfish has a higher tolerance for errors. The study was funded by the US National Science Foundation and National Institutes of Health.