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Predictive Patterns, Institute for Genomic Research, Millennium Pharmaceuticals, Michigan Life Sciences, Silicon Genetics, Lion Bioscience, Digital Data Management Corporation, Ocimum Biosolutions

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Predictive Patterns Licenses Molecular Mining’s Software

Predictive Patterns Software, a new company founded by former managers at Molecular Mining, said last week that it has licensed the rights to sell, support, and develop new versions of Molecular Mining’s GeneLinker product line from Parteq Innovations — the Queen’s University’s technology transfer company that took over management of Molecular Mining’s assets after it ceased operations in March.

Tom Radcliffe, president, and Mark Chatterley, vice president, served as director and manager of software development, respectively, at Molecular Mining.

Predictive Patterns said it would use the internet as its primary sales channel, rather than sales representatives, in order to keep costs down and price GeneLinker Gold “at less than half the price of other entry level gene expression analysis products,” Chatterley said.

 

Rice data Proves that Gene Finders Prefer Finished Sequence

The discovery of twice as many genes in the finished sequence of rice chromosome 10 than were predicted in the draft sequence “clearly demonstrates the importance of finished sequence,” according to Robin Buell, who leads the rice genome sequencing team at the Institute for Genomic Research.

The sequence and analysis of the smallest rice chromosome, published in the June 6 issue of Science, includes a predicted 3,471 genes — about 1,700 more than were initially predicted in the draft sequence.

Buell told BioInform that the same set of ab initio gene finders were used in both cases — in particular Fgenesh from Softberry. “The main difference,” according to Buell, “is that in the draft sequence, since the sequence quality is not as high as [in] finished, you don’t spend a lot of time manually adjusting all the models.”

So why did the rice gene count go up while the human gene count seems to keep going down with each new assembly? Buell said that one reason is that the contigs for the rice draft sequence were too short to anchor predicted genes to particular chromosomes. If anything, the gene predictors would have detected more genes in the draft, because the large number of gaps often splits genes into multiple exons so that they are counted twice or more by gene finding programs. But without a chromosome to assign them to, these “genes” went uncounted the first time around.

Buell said she’s confident that her team caught all the genes on the chromosome “because our estimate of gene density is very similar to what’s been found in other parts of the rice genome and we’ve also done enough searches of the sequence against various databases to see if there are any orthologs or homologs present. I don’t think it’s going to be like in the human, where there’s lots of question as to what’s going on.”

 

Millennium Drastically Scales Back R&D

Millennium Pharmaceuticals said last week that it will lay off an additional 600 staff and phase out its Cambridge, UK, and South San Francisco operations in a move to focus its resources more tightly on drug development and commercialization.

The bulk of the layoffs will occur in research, especially in early-stage discovery, the company said.

Mark Levin, Millennium’s CEO, said in a statement that the company has “reinforced its commitment” to bring products to market. “However,” he added, “We realize that to keep delivering on this commitment we need to focus more sharply on the most attractive opportunities in our pipeline. Unfortunately, this means that we will no longer have roles for many outstanding individuals who have made significant contributions to the development of the company.”

The layoffs will take place before the end of 2004.

 

Bioinformatics Benefits from Michigan Life Science Funding

Bioinformatics projects and companies supported by the Michigan Life Sciences Corridor are breathing a sigh of relief, having narrowly escaped a proposed funding cut of more than 56 percent in 2003. The state announced on May 28 that it would award $30 million in funding for 18 projects in 2003 — less than the $45 million originally earmarked, but not as small as the $20 million originally proposed in response to the state’s fiscal crisis.

The funds, to be disbursed from the state’s $1 billion in tobacco settlement money, include $6.8 million for bioinformatics projects.

The year’s largest single award provides more than $3.5 million for a project at Wayne State University to integrate bioengineering and bioinformatics to advance computer-assisted surgery research.

In addition, systems biology software startup GeneGo was awarded $1.4 million to develop a platform technology for the in silico reconstruction of disease states, and DNA Software was awarded $364,000 to commercialize its software for microarray analysis and PCR assay design. The Michigan Center for Biological Information — a bioinformatics core facility at the University of Michigan — was granted $1.6 million.

The Michigan Life Sciences Corridor steering committee also created a $2 million emergency fund to assist Pfizer scientists and professionals laid off after the company’s acquisition of Pharmacia.

 

Lion and Silicon Genetics to Integrate, Co-Market Software

Silicon Genetics and Lion Bioscience have entered a multi-year joint development and marketing collaboration centered around the integration of their software.

Initially, the integration will allow users of Silicon Genetics’ GeneSpring gene expression analysis platform to access data stored in Lion’s SRS integration platform. This will allow scientists to include information from both public and proprietary sources in their gene expression analysis, the companies said.

Lion will also integrate GeneSpring with its upcoming Target Engine drug discovery software platform, and will be able to co-market GeneSpring along with SRS and Target Engine.

 

DDMC to Distribute Redasoft’s Visual Cloning 3 in Japan

Digital Data Management Corporation (DDMC) will be the exclusive distributor of Redasoft’s Visual Cloning 3 software in Japan, Redasoft said last week.

Osamu Kobayashi, DDMC’s president and CEO, said that the company has a strong customer base in organic and inorganic chemistry, but has been “looking for a chance to expand our business to the biotechnology field, which is rapidly growing in Japan.”

 

Ocimum Sells Software to Dow AgroSciences

Ocimum Biosolutions said it has sold two licenses for its newly launched OptGene gene optimization software to Dow AgroSciences.

The software “enables design of genes with optimized features for expression in an organism of choice,” according to the company.

Filed under

The Scan

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Test for Them All

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PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

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