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Genome assembler
Computer program developed by Xiaoqiu Huang used to assemble the
genomes of the chicken, mouse and chimpanzee.
It took Xiaoqiu Huang two years to develop the initial version of PCAP (Parallel
Contig Assembly Program).
That initial version was used by Huang to assemble a mouse whole genome
data set on a cluster of Compaq ES40 servers. The assembly used a release
of the public whole genome shotgun data that was produced by the Mouse Genome
Sequencing Consortium.
While the mouse genome had already been assembled with other programs, Huang's
work, which is funded by the National Human Genome Research Institute of
the National Institutes of Health, proved that PCAP was an effective computer
program in sequence assembly.
Sequence assembly software such as PCAP is used by scientists to determine
the sequence of a long segment of DNA. In a shotgun sequencing project,
a long segment of DNA is cut into shorter and more manageable fragments
that can be read by current technology.
"Once we know the sequence of each fragment, we need to reconstruct
the larger sequence from the pieces," said Huang, associate professor
of computer science and an affiliate of the Plant Sciences Institute. "There
are so many pieces that need to be used for reconstruction of the original."
That's where programs like PCAP come in.
At Iowa State, Huang leads one of only a handful of nation-wide research
groups working on sequence assembly programs. He primarily works with the
Washington University Genome Sequencing Center in St. Louis, one of the
top genome sequencing centers in the world.
"I've continued to make improvements in PCAP," Huang said. "I
work with the researchers at Washington University to make revisions in
PCAP. They use the program and then give me feedback.
"I've lost count of the number of revisions we've made in the program
since the initial version."
Washington University researchers have used PCAP to complete an assembly
of the genomes of both the chimpanzee and late last year the chicken. Results
of the chicken genome assembly were published in the December issue of Nature.
PCAP has also been used for genome assembly of the fly, the worm and several
fungi.
Programs like PCAP allow researchers to dramatically reduce the costs and
time needed to assemble the genomes of the chicken and chimpanzee. Huang
estimates that while it cost $3 billion to assemble the human genome, costs
for the chicken genome are only $10 million - even though the chicken genome
is one-third the size of the human genome.
"PCAP took less than a week to produce the assembly of the chicken
genome," Huang said. "Our goal is to continue to make PCAP more
efficient, more accurate with more functions and features."
Huang says that while Washington University has used other similar programs,
PCAP has proven already to be more efficient and able to handle large genome
structures.
"I have been in this area for many years," he said. "Even
though my training isn't in biology, I know the problem and have a strong
computer science background that allows me to do the necessary programming."
Around LAS
February 21 to March 6, 2005
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