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Apr 1, 2009 (Vol. 29, No. 7)

Digital Gene-Expression Profiling

Technology Set to Compete with Microarrays in This Application Arena

  • Sequence Assembly Solutions

    Click Image To Enlarge +
    Clusters of interest within Heat Maps generated with DNAStar’s ArrayStar software can be selected and stored as gene sets for additional evaluation.

    DNAStar recently introduced QSeq, the first product to use the company’s disk sort alignment (DSA) algorithm for quantitative RNASeq applications and digital gene-expression experiments.

    “I believe that RNASeq is in the validation stage now,” says Tom Schwei, vp, GM, and CFO of DNAStar. “As we prove that the sequence-based techniques are at least as good as, if not better than the microarray-based techniques, there will be more uptake of RNASeq and digital gene expression. I think that component of microarrays [gene-expression analysis] will go down proportionally as the RNASeq methods gain acceptance.”

    DNAStar also introduced a beta version of SeqMan NGen (SNG), which can support next-generation sequence assembly on multiple instruments, including those of Illumina, Roche/454 Life Sciences, and Helicos, as well as Sanger sequencing data. The SNG algorithm assembles genomic fragment data up to 150 megabases in size and integrates with Lasergene sequence analysis software for sequence analysis and visualization.

    SNG can assemble an entire human chromosome, according to Schwei, and the largest project the company has tackled so far is human chromosome 8, assembling 150 megabases (of Roche/454 sequence data) with 7x coverage on a desktop computer in less than three hours.

    “We believe the software will be able to handle 30–50 megabase genomes on a template basis with 10 to 20 times coverage,” Schwei says. He emphasizes that the algorithm can be used for either template or de novo type sequencing projects.


Readers' Comments

Posted 04/07/2009 by Real Research

I study the above DGE technique. its amazing technique and i need traning in this technique i request to scientist please help i ever forget your this kind of help.

Research Officer
Ali Mohammad Dahri
Plant tissue culture labs,
PCSIR Labs Complex
Karachi

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