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Invitrogen, The Rat Genome Sequencing Consortium, Catapult Consortium

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Invitrogen Secures 86 Percent of InforMax Shares

Invitrogen said last week that InforMax share-holders have tendered about 86 percent of the company’s outstanding shares to it so far, a key step to wrapping up its $42 million purchase of the company.

Invitrogen said it needed 85 percent to complete a “short-form” merger that won’t require approval by a vote of shareholders.

InforMax shareholders who accepted the offer received $1.36 per share — a premium of 143 percent over InforMax’s share price when the deal was announced last month.

Invitrogen also extended the tender offer to Dec. 4. The offer was originally scheduled to expire on Nov. 22.

 

Atlas Assembly Algorithm Puts Rat Sequence Together

The Rat Genome Sequencing Consortium, led by the Baylor College of Medicine Human Genome Sequencing Center, said last week that it had wrapped up the 21-chromosome assembly of the rat genome.

The international consortium of researchers from eight companies, hospitals, and academic and non-profit groups used a hybrid of clone-by-clone sequencing and whole-genome shotgun sequencing on the rat, which required new assembly software, called Atlas.

Rui Chen, an assistant professor at Baylor who led the group that developed Atlas, told BioInform that his team began developing the software when there were no other publicly available methods for assembling whole-genome shotgun data, so it was written concurrently with Arachne from the Whitehead Institute and Phusion from the Sanger Institute.

While all three methods do have a few similarities, Chen noted that Atlas was designed specifically for the hybrid sequencing strategy used for the rat genome sequence, and therefore is better suited for the combined BAC and whole-genome shotgun data than Arachne, which works only on WGS data.

For BAC-end sequencing, “you need to deal with a lot of quality control in clone generation. There’s a lot of human error.”

Atlas is based on Phrap, and is more closely related to the Phusion assembler from Sanger than it is to Arachne, Chen said. The Rat sequencing consortium plans to use Phusion on the next version of the rat assembly, with the goal of comparing the two assembly approaches in order to improve upon them.

Parts of the Atlas assembler are currently available through Baylor’s BAC-Fisher page at http://www.hgsc.bcm.tmc.edu/BAC-Fisher/, but Chen said the developers are working on an improved version of the software that will be released in February or March, 2003.

Chen said his team is currently writing a paper on the Atlas assembler.

Assembly of the 6.5-fold coverage, around 33 million gene sequences, took around 10 days, Chen said. The rat genome is about 2.8 gigabases — slightly smaller than human but larger than mouse.

 

Catapult Wants to Train IT Guys (and Gals) on the Nuances of Life Science

The communication gap between IT professionals and bioinformatics scientists is growing, according to the Catapult Consortium, and the Wildwood, Mo.-based consulting firm wants to do something about it.

The company plans to offer a series of low-priced tutorials that IT specialists — whether executives, developers, or sales and marketing types — can download from the internet to brush up on the subtleties of the life sciences.

Catapult president Rebecca Hyman said that most of the company’s clients currently come from non-scientific backgrounds and are seeking a leg up on everything from the basics of biology to higher-level questions about bioinformatics algorithms.

“IT managers working with life science researchers need to understand what they’re doing,” Hyman said. “They’re not sure how to budget for staff, how to evaluate their technical resources, what to look out for in terms of hardware and software trends.”

The company is putting together a series of online tutorials that will range from $30 to $50 to answer the most frequently asked questions IT professionals would have about bioinformatics.

Bioinformatics scientists and professionals write the tutorials under a profit-sharing arrangement, and Hyman said that the company is seeking submissions from authors interested in preparing a lesson on a topic of their choice.

The first of the tutorials is scheduled to launch in January.

Further information is available at: http://www.catapultconsortium.com/index.html.

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