An ISU professor has taken one of the top spots in genetic research, earning international acclaim both for himself and Iowa State.

Xiaoqui Huang, associate professor of computer science, is well known in the international genome assembly community for his work with genetic sequencing programs, primarily for his Parallel Contig Assembly Program.

PCAP is a sequence assembly software used by scientists to determine the sequence of a long segment of DNA. Huang said his goal is to develop an effective and efficient program for reconstructing the genomes from short sequences into long sequences using computers.

A person’s DNA is composed of a series of substances, called bases, that are used like a code to determine personal attributes. There are four bases used in DNA, and the order of the bases is important.

Shiaw-Pyng Yang, research assistant professor at the Genome Sequencing Center in the Department of Genetics at the Washington University School of Medicine in St. Louis, said his department has been collaborating with Huang for about three years on what he calls a very efficient program.

“Dr. Huang has developed very good algorithms, called PCAP, for the genomic fragments assembly,” Yang said.

Huang said he has been working with genome assembly for 13 years, first in small-scale sequencing projects at a previous school and now in large-scale sequencing at Iowa State. It took him two years to develop the PCAP.

PCAP allows researchers to cut the costs and time needed to assemble the genomes of animals and plants.

Huang said efficient technology would lead to remarkable advances in biology, medicine and agriculture. Yang said because of the PCAP, a number of genomes ranging from bacteria to mammals have been assembled.

There have also been significant advances in chicken and chimpanzee genomes, taking less than a week to assemble the chicken genome, Huang said.

A genome assembly program inputs short sequences and combines them into long sequences based on similarities and other relationships between short sequences. Although researchers take special precautions, the program sometimes makes mistakes combining sequences that do not really belong together.

Huang compared the process to finding and fitting together puzzle pieces.

His program is one of half a dozen in the field. All of the programs share similarities but have different engineering details, Huang said. He said he encourages diversity in the field because no program is perfect.

“Each program has its own strengths and weaknesses,” Huang said.

He said he continually makes changes and believes it is crucial for the developer and user of a program to have a close working relationship in order to better pinpoint needed improvements.

Qunfeng Dong, assistant scientist for genetics, development and cell biology, said PCAP has been instrumental in the his department’s work with corn and other plant species.

Dong said that, in the computer science field, Huang’s programs are well known and widely used in processing of DNA data, an accomplishment most computer scientists never attain.

“He has an impact on the field,” he said.

Yang agreed and said Huang is one of the best genome assemblers in the world.