Long-range genomic patterns
ecec at midway.uchicago.edu
Wed Mar 24 11:02:47 EST 1993
In article <9303201442.AA02197 at net.bio.net> pigliucc at uconnvm.bitnet (Massimo Pigliucci) writes:
> Dear Compunetters,
> in response to Mike Levin's request
>about long-range genomic patterns, there are two types of studies
>that I'm aware of (I'm not a molecular biologists, by the way):
>the search for long-range correlations in DNA sequences through
>algorithms capable of locating fractal (i.e., scale-invariant)
>features. A brief review of recent attempts is in Amato, I.
>Science 257:747 (1992), but you might want to check several of
>the latest issue of Science.
> I'm more familiar with the second approach, because James
>Lyons-Weiler and Don Les at the University of Connecticut are
>working on it. It encompasses the use of Chaos Game
>Representation algorithms (again, for the identification of
>fractal patterns) on sequences of the same gene in different
>organisms or of related sequences in the same taxon. The first
I saw the Chaos game representation in either Science or Scientific
American and immediately rushed to the keyboard to adapt a mouse-driven
version of the Chaos game into one that could read DNA sequences.
And it looked terrible! So then I tried various modifications including
comparisons of several sequences. Nothing gave a pattern much different
than the ones I got using randomly generated sequences. Rather than
give up and get back to work, like a sensible person, I pursued the
Chaos game representation to what I considered the ulitimate degree.
Instead of using the entire screen I used a small region for the coordinate
system. Then that was shifted to the right for each new residue. Rather
than just draw the points, a line was extended between each point and
its successor. The representation of multiple (in this case aligned)
sequences was accomplished by drawing in each in a different color.
And the result, you guessed it, it looked like randomness.
U. of Chicago
Eric Cabot | "Non Nobis Nati Solum"
ecec at midway.uchicago.edu |
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