Biology Application Brief
Dr. Dan Davison at the University of Houston is using DADiSP
examine the human beta-hemoglobin gene complex for these long range
periodicities. The method used to accomplish this is fairly simple and
straight forward. The DNA sequence is first encoded (A=1, C=2, G=3,
A plot of the delta gene from the beta-hemoglobin complex is generated
and displayed in Window 1. An area is then selected containing just
the coding region with no upstream or downstream regions.
The encoded region is subsequently run through the Spectrum routine on
the FFT menu in DADiSP. Because the delta gene is a coding region, the
resultant graph in Window 2 shows a prominent peak at 0.33,
corresponding to a periodicity of 3. This corresponding group of three
nucleotides is biologically referred to as a codon, part of the protein
coding region. Thus DADiSP can effectively be used to detect coding
regions in DNA, an important problem in molecular biology.
DADiSP can also be used to interpret other features in the DNA. The
group of three peaks around 0.10, 0.11, and 0.12 in Window 2 are a
measure of the simplest helical turns in DNA, which average 11
nucleotides per turn.
Some of the other peaks correspond to multiples
of the 0.3 and 0.11 peaks. There is also a strong peak above the
vicinity of 0.01 which is an echo of how the DNA is wound around a
group of proteins known as the nucleosome. The nucleosome plays an
important part in how the DNA is packed into the chromosomes in every
Unraveling the Human Genome
In this way DADiSP can enhance the unraveling of the human gene
complexes and perhaps provide a tool for unlocking the mysteries of how
DNA controls the diversity found in life. According to Dr. Dan
Davison, "DADiSP makes this kind of analysis very easy to do, so that I
only have to worry about the science, not the programming."