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CompugentoLaunchToolforIdentifying Proteins; Says Low Gene Count Validates Efforts

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Compugen is planning to launch a new Internet-based automated protein identification tool in the second quarter of this year that will be designed to identify proteins based on data generated by mass spectrometers.

Michal Preminger, Compugen’s vice president of proteomics, said researchers will be able to submit their data to Protocall, which will be accessible through Compugen’s LabOnWeb portal. The system will then seek to match the data to one of the 160,000 known human proteins that currently exist in Compugen’s database.

“We have an obvious advantage with our Leads database,” said Preminger. “We have four times the available proteins that exist in public protein databases. And our database is updated continuously.”

Compugen’s database also contains thousands of proteins identified in mice and rats.

Preminger said that Compugen of Tel Aviv, Israel, built its database by modeling alternative splicing patterns, which enabled the company’s researchers to sequence a relatively large number of proteins. She added that Compugen also developed advanced algorithms to extract information from data generated by mass spectrometers.

Compugen, which will also offer users some annotation information, albeit less than SwissProt, will provide a link to genomic data the company has generated. Together, this could help to shed light on possible protein function as well as assist downstream in the drug discovery process, Preminger said.

Preminger noted that the company would aim to sell Protocall, which is currently being beta tested by a few potential users, to smaller biotech and genomics companies rather than big pharma.

“We won’t try to convince big pharma to put their data on the Web,” Preminger said. “Instead, we’ll market to the many organizations who are comfortable using the web and eventually we will offer an installable version of Protocall.”

Big pharma is generally wary of using Web-based products for fear that non-authorized people would be able to gain access to their data.

Preminger did not say when the installable version of Protocall would be available. Protocall will likely be available on a subscription as well a fee-per-use basis.

In addition to Protocall, Compugen is also making a big push to sell access to its Gencarta database, which includes genomic, proteomic, and transcriptomic data. The company said that Celera’s recent announcement that it found only 30,000 genes in the human genome supported its own belief that alternative splicing accounts for the far greater number of proteins than genes.

“[The] release of the sequence of the human genome supports Compugen’s position of the past four years that alternative splicing is the rule and not the exception,” said Mor Amitai, CEO of Compugen. “Our understanding of this phenomenon positions us as the leading company in the understanding of the transcriptome, the missing link between the genome and the proteome.”

The company recently set up a California-based sales office to beef up its West coast marketing efforts and also plans to build a bigger presence in Europe.

—JF

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