order on the DNA.
Until now, generally available computer programs have had to test every
possible combination of locations for each set of these DNA signposts to
figure out which one was correct. This method takes a large computer a relatively
short amount of time if processing only 15 or 20 markers. However, each
of the human chromosomes contains 500 to 1,000 of these markers -- far too
many to map all at once using available computer programs.
To solve this problem, computer scientists at the Stanford Human Genome
Center applied a well-known computer trick: They instructed the computer
to ignore some unlikely possibilities instead of demanding that every possibility
be checked.
"This technique is not exact or exhaustive -- and that's why it works.
The computers don't try everything -- that would take forever -- but they
come up with pretty good answers," said Kathleen McKusick, computer
scientist at the Stanford Human Genome Center. She and Cox played the major
roles in developing the new computer program.
To create Mapper, the scientists started with a very thorough program developed
by Michael Boehnke at the University of Michigan. But that program eventually
fell by the wayside.
"We built a car around an engine, and then changed the engine,"
said McKusick.
McKusick and colleagues modified the original program in steps, gradually
replacing the very precise, but time-consuming and expensive parts. At every
point, they evaluated its success to make sure they were not sacrificing
accuracy.
"We started out using the off-the-shelf thing, then tried to scale
it up. We found that we were bumping up against its limitations -- then
we'd change it. Eventually, the original program just dropped out of the
picture," said McKusick.
So far Mapper is performing well, she said. The researchers have tested
Mapper's accuracy by comparing its results with genetic maps obtained by
other scientific methods.
'"/>Contact: Mike Goodkind
ma.meg@forsythe.stanford.edu
Stanford University Medical Center 13-May-1996Page: 1 2 3 Related biology news :1.
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