Scientists develop open-source genome analyzer

Posted by Chris Nova

Scientists at Albert Einstein College of Medicine of Yeshiva University have developed a desktop genome analyzer.

It works in conjunction with a browser that allows biologists to rapidly and easily analyze and process their high-throughput information. The open-source software is called GenPlay, and it’s described in the May 19 online edition of Bioinformatics.
    
Presently, genomic data is examined mainly by information specialists instead of the biologists who planned the experiments that produce the data. GenPlay was created because biologists needed a user-friendly, multi-purpose tool that can aid them in visualizing, analyzing and transforming their raw data into biologically relevant tracks.
    
“The first human genome was sequenced 10 years ago by an international consortium at a cost of $7 billion,” notes GenPlay co-developer Eric Bouhassira, Ph.D., senior author of the Bioinformatics article, professor of medicine and of cell biology, and the Ingeborg and Ira Leon Rennert Professor of Stem Cell Biology and Regenerative Medicine at Einstein.

“But today, a complete genome can be sequenced for less than $10,000 and the cost is predicted to drop to less than $1,000 in a few years. The dramatic dip in cost has led to the creation of an avalanche of new data that biologists are having trouble analyzing. GenPlay is intended to make it easier for biologists to make sense of their data.”

There are about a dozen genome browsers that are currently available. GenPlay has a major advantage over the others, says Dr. Bouhassira, because it “emphasizes letting biologists take control of their own data by providing continuous visual feedback together with extremely rapid browsing at every decision point during an analysis.”

GenPlay is compatible with three major types of data: data from gene expression studies, epigenetic data, and single nucleotide polymorphism (SNP) data. The free GenPlay software is available online.

The Bioinformatics paper is titled “GenPlay, a Multi-Purpose Genome Analyzer and Browser.” The main author of the paper is Julien Lajugie, M.S., associate in Einstein’s department of medicine, who co-developed GenPlay and wrote the GenPlay program.