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PipMaker Developer Anticipates Spurt in Demand for Comparative Genomics Server

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Penn State University’s Webb Miller is gearing up for an expected jump in hits to his PipMaker sequence alignment server over the next year.

With the near completion of the human genome and the steadily increasing sequence data flow for other organisms, Miller expects comparative genomics to be a primary component of post-sequence genomics.

“I think we get a lot of use right now, but in a year it’s going to be a lot higher,” Miller said. “The public effort is supposed to have 3x of the mouse done by May. That’s enough to start assembling it, so I think my server is going to be very popular soon.”

Miller’s server was initially launched in July of 1999 to align two similar genomic DNA sequences. Users can submit information such as sequence, gene location, or other annotation information, and the server aligns them and sends the user a visual representation of the alignments in several formats.

One display is a percent identity plot (pip), which indicates the degree of similarity for each aligning segment in a color-coded format: yellow for a sequence in one species not found in the other species, red for a sequence in one species whose immediate neighbor has a homolog elsewhere in the other species, blue for a sequence in one species whose immediate neighbor has no detectable homolog in the other species, and gray for areas not sequenced in the other species.

Miller plans to release a multiple sequence server, MultiPipMaker, by May. He said the Penn State Bioinformatics Group is also involved in a project to sequence selected regions from 12 vertebrates — human, chimp, baboon, dog, cat, pig, cow, chicken, mouse, rat, zebrafish, and fugu. The new server will be able to align 12 sequences or more at a time, Miller said.

Use of the server is currently free. Because commercial users are reluctant to send their sequence data to an off-site server, he said plans are in the works to develop software that can be run on client sites.

Miller doesn’t foresee any difficulties in keeping up with the anticipated volume. “We have a ways to go before we saturate our workstation,” he said.

“If I have to go to more computers, that will be good news,” Miller added.

The project is funded by a grant from the National Human Genome Research Institute.

PipMaker is available at http://bio.cse.psu.edu.

— BT

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