Communications of the ACM
Computational Method Dramatically Speeds Up Estimates of Gene Expression, CMU, UMD Researchers Report
Researchers announced Sailfish, a new computational method that dramatically speeds up estimates of gene activity from RNA sequencing data.
Credit: Shawn Heinrichs
Researchers at Carnegie Mellon University (CMU) and the University of Maryland say they have developed a computational method that dramatically speeds up estimates of gene activity from RNA sequencing data.
The method, called Sailfish, makes gene expression estimates in a few minutes, compared to the several hours it takes other conventional methods. The researchers found they could allocate parts of the reads to different types of RNA molecules, as if each read acted as several votes for one molecule or another. Without the mapping step, Sailfish can compete an RNA analysis up to 30 times faster than previous methods.
In addition, the researchers say the Sailfish method is better able to tolerate errors in the reads or differences between individuals' genomes. The errors can prevent some reads from being mapped, but the Sailfish method can make use of all the RNA read votes, which improves the method's accuracy, according to CMU professor Carl Kingsford.
From Carnegie Mellon News
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