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BIOINFORMATICS BRIEFS: Jun 3, 2002

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Celera Deposits Mouse Chromosome 16 Sequence in Genbank…

Celera Genomics published a comparison of its whole-genome shotgun-derived mouse and human sequences in Science last week in a study that highlighted the similarity of mouse chromosome 16 with homologous segments on human chromosomes 3, 8, 12, 16, 21, and 22.

In addition, the company deposited the sequence of Mmu 16 into Genbank under accession number AAAD00000000.

The company also created a web page (www.celera. com/mouse16) “to offer researchers easy access to the mouse chromosome 16 sequence data as well as additional data and information not covered in the Science publication and not deposited in Genbank.”

According to Celera, the mouse assembly and annotation appearing in Genbank and used in the Science paper is based on the original assembly the company made available to customers in July 2001. The company has since released an updated assembly with more than 7.9X coverage from four distinct strains and 1 sub-strain.

Celera identified 731 protein-coding genes on mouse chromosome 16. Of these, approximately 98 percent had a human counterpart. Only 14 genes of the mouse genes on this chromosome had no counterpart in humans.

 

…and Collaborates with Ensembl on Mosquito

Celera also lent a hand on the annotated draft of Anopheles gambiae (African mosquito), which was released through Ensembl last week at www.ensembl.org/Anopheles_gambiae.

Celera collaborated with NIAD-NIH and Genoscope on sequencing the genome and with Ensembl on an annotation set of protein coding genes. Through Ensembl, users will have access to the Celera assembly and joint Celera/Ensembl annotation set, with initial functional analysis through Interpro.

 

Spotfire and Rosetta Integrate Platforms

Spotfire and Rosetta Biosoftware said last week that they would integrate their DecisionSite and Resolver technologies. In addition, Rosetta plans to offer customized integration of the two products through its professional services business as part of the agreement.

Under the three-year deal, current and future customers who subscribe to the platforms will be able to use both products simultaneously to analyze gene expression data. Currently, the companies share customers including Abbott, Aventis, GlaxoSmithKline, Merck, and Monsanto.

The integration will be available as early as July at no additional cost to customers who use both tools. It will take place either over the Internet or through an installation process, said David Butler, vice president of product strategy and marketing at Spotfire.

 

UC Irvine Wins Bioinformatics Training Grant

The Institute for Genomics and Bioinformatics at the University of California, Irvine, has been awarded a multi-year $4.3 million grant from the National Institutes of Health to expand its bioinformatics training program into a campus-wide initiative.

The new biomedical informatics training program will combine work at the Institute for Genomics and Bioinformatics with current efforts in the university’s Department of Information and Computer Science, College of Medicine, School of Physical Sciences, and School of Biological Sciences.

The Department of Information and Computer science launched UCI’s informatics in biology and medicine graduate degree program in 1999. Plans for the NIH grant call for mirroring this program in the College of Medicine and the School of Biological Sciences.

Pierre Baldi, a co-director of the program, said that “interdisciplinary graduate programs in bioinformatics remain scarce and the pool of individuals with training in both computational and biological sciences is exceedingly small.” In order to address this need, Baldi said the biomedical informatics training program gives students access to dual advisors one each in computational sciences and life sciences.

 

Nonlinear Gains Traction in Asia-Pacific Market

Nonlinear Dynamics of Newcastle-upon-Tyne, UK, said last week that it has appointed Taipei-based J & H Technology as the exclusive distributor in Taiwan for its Phoretix software products.

The agreement follows on several distribution agreements the company has signed with Asian companies: In early May Nonlinear selected Chayon Laboratories as its exclusive distributor in Korea for Phoretix, and in March it tapped Tomy Digital Biology as the exclusive distributor for Phoretix in Japan.

In addition, Nonlinear said last week that under a non-exclusive worldwide distribution agreement it signed in 2001 with PerkinElmer Life Science, the companies sold two Progenesis 2D gel software systems to the Yonsei Proteome Research Center in Korea the first sale of the product in the Asian region.

Taiwan’s J&H Technology specializes in reselling instrumentation and other supplies for proteomics research. In a statement, James Tsai, CEO of J & H, said, “The scope of funded research programs in proteomics and genomics is expanding rapidly in this country, and Nonlinear’s products will allow us to improve our service to our customers accordingly.”

The Yonsei Proteome Research Center at Yonsei University in Seoul, Korea, plans to use its two Progenesis systems as a key component of a “fully automated clinical proteomics information database” it is developing.

 

Compugen, Genomic Solutions Drop Arthur Andersen

Compugen and Genomic Solutions have both replaced Arthur Andersen as their independent auditor in favor of Ernst & Young.

Compugen, which used Arther Andersen member firm Luboshitz Kasierer to audit its 2001 financial results “has moved to work with Ernst & Young,” said CFO Nurit Benjamini via e-mail.

Genomic Solutions issued a statement on its decision to replace the embattled accounting firm. “We conducted a comprehensive review of several highly respected independent audit firms and we are confident that Ernest & Young is a good selection for Genomic Solutions,” said Steven Richvalsky, CFO.

Arthur Andersen is currently on trial in Houston on a charge of obstruction of justice for its destruction of thousands of documents related to its work for Enron.

 

ADA to Use UD’s Metaprocessor for Diabetes Research

United Devices of Austin, Texas, said that the American Diabetes Association has selected its MetaProcessor distributed computing platform in a diabetes-related research project.

The platform will run the Archimedes clinical program software application developed by Kaiser Permanente on a 250-PC enterprise grid, which will also serve as the test bed for further development of the Archimedes application.

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