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Computational Genomics Conference BLASTs Off

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This year’s Conference on Computational Genomics in Baltimore began with a BLAST.

Warren Gish of Washington University, co-author of the original 1990 paper describing the ubiquitous sequence similarity search program, opened the fourth annual TIGR meeting last Thursday with a tutorial on recent developments in the program.

The Washington University version of the program has been revised to handle the vast amounts of sequence data now available. With the contents of GenBank exceeding two gigabytes, a single-query search of the entire database using the older program on a 32-bit computer has become a problem. Gish explained, among other things, how to run the updated BLAST program on a standard PC.

But the meeting quickly turned from academia to business. Although the conference is more focused on academic issues than its big sister GSAC, commercial issues are seeping in.

Biotech intellectual property law expert Paul White of Pillsbury Madison & Sutro led the tutorial that immediately followed, "Legal Protection for Your Bioinformatics Technology."

"This year we thought that would be a timely topic," said Steven Salzberg, conference co-chair and director of bioinformatics at TIGR. "Many people in the academic sector are involved in small companies or spinning off companies, so we’re certainly more interested in that."

Another issue that bioinformaticists are certainly more interested in this year, as the number of talks devoted to the topic signifies, is microarray analysis. As the use of microarrays becomes more popular, researchers are grappling with ways to make sense of the thousands of data points generated from a single experiment.

And with 30-plus genomes now sequenced, comparative genomics, and gene-finding were also hot topics.

Despite the focus on computational methods and algorithms, there was significant attention on bioinformatics from the biological perspective. For example, two biological researchers — Daniel Carucci of the Naval Medical Research Center and Ken Stuart of the Seattle Biomedical Research Institute — held a workshop on parasite bioinformatics with presentations on the biology of two model organisms: the malaria pathogen and Leishmania. Their talks were then followed by a look at computational work on those organisms.

Two of the keynote speakers at the conference, Gerald Rubin of University of California, Berkeley and Mark Adams of Celera Genomics, are biologists.

"One of the things that identifies this meeting and distinguishes it from other bioinformatics meetings such as ISMB and Recomb is that we’ve been trying since its inception to have a more biological focus," Salzberg said.

—Aaron J. Sender

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