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Sequence Gazing

May 15, 2007 | The prodigious output from next-generation sequencing platforms offers exciting opportunities for sequence software specialists too. Tom Schwei, general manager of Madison, WI-based DNAStar, says that for almost 20 years, his company’s Lasergene software has “done a nice job of the ‘blocking and tackling’ of sequencing analysis” — sequence assembly, analysis, gene identification, and visualization. “We’ve been there, we’re still there, and we’re going to be there. It’s incredibly important to scientists using our product.”

Schwei says the most recent release of Lasergene had “a powered up assembly engine aimed at areas where next-generation sequencing is coming into play — taking Sanger data and complementing those with 454 data, and finding ways to do successful assemblies.”

While Lasergene is primarily a desktop tool useful for modestly sized genomes, DNAStar is developing a new genome assembler tool, currently in alpha testing with a couple of labs, including GATC Biotech in Germany (it recently purchased 454 and Solexa instruments.) “This could be powered up on a Linux cluster to handle larger organisms,” says Schwei. It takes better advantage of paired-end reads, using them for assembly, not just alignment. And “Because of the way the processing algorithm works, it processes several times faster than Lasergene. If you can use clusters, you will ultimately be able to do even greater than that.”

“Our philosophy is we want to be able to work with all the kinds of data out there. The closer our realationship to the manufacturers, the better. We’re not looking to replace the software they distribute... that’s not our goal. But we expect great value to end users as software that can handle 454, Solexa, Applied Bio, Helicos, and Sanger,” says Schwei.

“If one software package can take all those types of data and work well with those, that’s a tool that will be very valuable to many scientists.” -- K.D.

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