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eCodonOpt, v1.0
Last Updated 04/23/02
ReadMe.txt
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Contents of eCodonOpt 1.0 distribution:

eCodonOpt is a two-phase computational framework. First, sequences (both
nucleotide and residue) must be transferred to GAMS input by preprocessing
them with 2 FORTRAN 90 codes. Then, with the new include files for GAMS,
the codon optimization is performed and new nucleotide sequences are
designed and output. Below are some notes on the two phases.

Phase 1 - FORTRAN 90 preprocessing:
  Two pieces of information are needed by GAMS: (1) the residue sequences,
  so it knows the set of nucleotide allowed at each position, and (2) the
  wild-type nucleotide sequences, so the number of mutations away from
  wild-type can be limited. The preprocessing/ directory contains
  two FORTRAN 90 programs for doing this. Two files are generated for
  GAMS: (1) allowed.inc and (2) originals.inc. Some samples of these
  include files can be found in the root directory. In addition, another
  include file containing information on the nearest-neighbor enthalpy
  and entropy parameters is found in the core_includes/ directory.

Phase 2 - GAMS codon optimization:
  Three GAMS codes are included (all in the root directory):
  1) eCodonOpt.gms - utilized for free energy minimization of any number
                     of parental sequences. Also can be used for minimizing
                     bias in family DNA shuffling by including upper and
                     lower bounds on free energies of parental pairs.
  2) positions.gms - utilized to position crossovers in specific regions
                     (e.g., loop, scaffold).
  3) metrics.gms - utilized for free energy minimization with constraints
                   on metrics (CAI, MCU) that account for host-specific
                   codon preferences.

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Contact Costas Maranas (costas@psu.edu) or
        Greg Moore (greg@cyprus.che.psu.edu) with questions and comments.

Also see:
Moore, G.L. & C.D. Maranas (2002), "eCodonOpt: A Systematic Computational
Framework for Optimizing Codon Usage in Directed Evolution Experiments,"
Nucleic Acids Research, in press.

http://fenske.che.psu.edu/CMaranas/
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