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longest matching sequence

Tom Schneider toms at fcs260c2.ncifcrf.gov
Mon Sep 30 08:26:22 EST 1991

In article <9109261841.AA15052 at bambi.ccs.fau.edu> tomh at BAMBI.CCS.FAU.EDU (Tom Holroyd)
> Waterman, M.S., L. Gordon, and R. Arratia.  Phase transitions in
> sequence matches and nucleic acid structure.  PNAS 84: 1239-1243, 1987.

> The phase transition they refer to is
> that the minimum energy, and thus the alignment selected, changes
> from a linear to a logarithmic relationship with the mismatch penalty.

How could an energy be involved when a human compares two sequences (other than
the actions that the human takes)?  That is, although I'm sure it takes energy
to compare sequences, what could this possibly mean in terms of the molecules

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms at ncifcrf.gov

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