BY BRENDA POLK
HOUGHTON--A Michigan Tech University researcher is working to develop a computer program for assembling DNA sequences.
Xiaoqiu (Siaochew) Huang, associate professor of computer science at Michigan Tech, hopes to reconstruct complete DNA sequences out of short sequence fragments. "Sequence data," says Huang, "is like a dictionary or source book for medical researchers.
"The DNA sequence information can help researchers study the genes encoded in the DNA. To determine gene location and understand gene functions within DNA, the entire DNA sequence must be reconstructed, though not physically."
"Sequencing machines" which determine the DNA sequence of short pieces, called fragments, produce the input data used in Huang's program. The program takes those 1,000 to 10,000 separated sequence fragments and puts them in their original order.
"False overlapping is the main difficulty," says Huang. Within a DNA structure there may be similarities at the ends of each fragment, like matching domino ends. Sometimes these unpredictable matches are a part of the actual DNA molecule.
Imagine a chain of dominoes with a four on its open end. There are two dominoes available, each with a four on one end, but different numbers for their other ends. One domino is meant to join the chain at the open spot, but the other will join the chain elsewhere.
Currently, determining which overlaps are meant to be connected is what takes the most time. When using Huang's program, researchers in the biological community will be aided by a sequencing assembly process that works quickly. As fast as knowledge of DNA molecules grows, researchers will be able to apply that information for society's benefit.
Working on his third version of this program, Huang has provided similar programs to over two dozen biology sequencing labs around the world. "Scientists from other labs have told us it is very helpful to their research," says Huang.
The project is being funded by a $150,000 grant from the National Institute of Health.