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A New Approach Uses Compression to Speed Up Genome Analysis


Compressing a dataset with specialized algorithms is typically done in the context of data storage, where compression tools can shrink data to save space on a hard drive. But a group of researchers at MIT has developed tools that compute directly on compressed genomic datasets by exploiting the fact that most sequenced genomes are very similar to previously sequenced genomes.

Led by MIT professor Bonnie Berger, the group has recently released tools called CaBlast and CaBlat, compressive versions of the widely used Blast and Blat alignment tools, respectively.

In a Nature Biotechnology paper published in July, Berger and her colleagues describe how the algorithms deliver alignment and analysis results up to four times faster than Blast and Blat when searching for a particular sequence in 36 yeast genomes.

"What we demonstrate is that the more highly similar genomes there are in a database, the greater the relative speed of CaBlast and CaBlat compared to the original non-compressive versions," Berger says. "As we increase the number of genomes, the amount of work required for compressive algorithms scales only linearly in the amount of non-redundant data. The idea is that we've already done most of the work on the first genome."

These two algorithms are still in the beta phase, and the MIT team has several refinements planned for future release to optimize performance. To that end, Berger has made the code for both algorithms available with the hope that developers will help them build "industrial-strength" software that can be used by the research community.

"To achieve optimal performance in real-use cases, we expect the code will need to be tuned for the engineering trade-offs specific to the application at hand," she says. "The algorithm used to find and compress similar sequences in the database may need to be tweaked to take this issue into account, and the coarse- and fine-search steps should be aware of these constraints as well."

While computing resources are becoming increasingly powerful, Berger contends that better algorithms and the use of compression technology will play a crucial role in helping researchers to keep up with the production of next-generation sequencing data.

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