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UPDATE: Celera Launches Celera Discovery System, Version 3

NEW YORK, Jan 18 – With the launch of Celera Discovery System version 3, the company hopes to provide subscribers with an integrated, annotated map of protein and genomic information that will pave the way for Celera to gain a foothold in the burgeoning proteomics sector, company executives and analysts said.

The new version of the database, which the company made available to current subscribers this week, provides the “foundation on which we will be able to lay proteomics data into the Celera Discovery System,” said James Peck, senior vice president of product development for Celera.

In CDS3, a user can view both gene and protein prediction on one map and have access to classification algorithms for protein families as well as a gene ontology program for classifying proteins. The update also gives researchers the ability to search for sequence patterns and similarities, conduct cross-genome comparisons, gain access to Celera’s computing power, and integrate data from 34 public and private databases, including Celera’s sequence of the D. melanogaster genome.

”What we’ve done is built a method for viewing all this information that will allow the user to navigate much more quickly and understand the research problems in context,” Peck said “They can perhaps determine [function or role] of a new protein by searching for that protein in similar domains that the company has built using proprietary protein classification technology.”

Celera is just beginning to assemble its own database of proteomic information, and has not decided whether or how to make this data available to subscribers. Bu the current database includes Proteome’s Bioknowledge library of searchable proteomics databases, which Celera acquired a license to before Incyte acquired proteome, and also has integrated proteomics data from public databases in CDS3.

In the past, some analysts have questioned the long-term financial viability of Celera’s subscription-based business model, and have pointed to the handful of private sector subscribers the company has so far signed on.

But analysts responded enthusiastically to the release of CDS3.

“Version 3 offers impressive flexibility,” said William Blair analyst Jonathan Good. “[It] has greatly expanded the different starting point to search for genomic information, which we believe makes the product more attractive to a wider range of potential customers.”

The user of CDS3 starts from the biomolecule start page and can browse through by clicking onto a map of a chromosome and then scroll across to locate markers and genes, according to Good. When a user clicks onto a gene, annotations to that gene, SNPs and links to proteins expressed by the gene come up. This search can also go from protein to gene to SNP.

Todd Nelson, an analyst at Dain Rauscher Wessels reiterated his “buy – aggressive” rating, pointing to the release of CDS3 as well as Wednesday’s announcement that Celera subsidiary Paracel has introduced GeneMatcher2, a supercomputer that can do high-throughput analysis of sequence similarity.

“We are encouraged that Celera continues to update and innovate its product line to provide leading information and computing solutions to its customers,” Nelson wrote.

Celera’s stock was up 2, or 5.1 percent, at 41 3/16 in late afternoon trading Thursday.

On the technology side, the new version of CDS does not yet incorporate the updated version of SRS that Lion Bioseciences is currently developing in collaboration with Celera. Lion is designing this expanded version of SRS to make the program capable of “scaling to the large data volume that Celera is beginning to generate in other areas besides the human genome,” said Christian Marcazzo, Lion’s director of product marketing. Lion expects to finish this new version in six to nine months, but does not know when Celera will formally incorporate it into CDS.

Celera says, however, that it has improved its efforts to facilitate integration of other companies’ proprietary databases into Celera’s system. The new version allows users to read in XML files into the database.

Another new feature of the update is the incorporation of mouse genome fragments into cross-genome comparisons. “We use the mouse as an annotation tool,” said Peck. “The mouse is helping us with our gene predictions.” Celera is still assembling the mouse genome fragments, and will likely have an internal version of the genome available by end of this month, according to Peck.

The next version of CDS, Peck said, will further integrate public and proprietary information from additional databases. " We believe literature annotation is an important component of what our users need to fully engage in research problems. We are working toward literature annotation products that will be annotated through CDS.”

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