                              codon-optimizer 0.1
(Reference implementation of a CAI optimizing and motif engineering algorithm)

                Written by Chris Thachuk <cthachuk@cs.ubc.ca>

  2012 Chris Thachuk <cthachuk@cs.ubc.ca>.  This software is distributed under 
  the GPL licence version 3 or greater.  Please see the file LICENSE in the 
  distribution for more information.


DESCRIPTION

  This software serves as a reference implementation of a dynamic programming 
  algorithm proposed by Anne Condon and Chris Thachuk in the paper:

        Codon Optimization with Motif Engineering.  Journal of Discrete 
        Algorithms, 2012.

  The codon optimization code was extracted from a larger oligo design for
  gene synthesis library (currently unpublished).

REQUIREMENTS

  To build the software, a C++ compiler is required, and the Boost libraries 
  version 1.48 or higher.
  
  To bootstrap from a Git checkout, or if you change the Automake files
  and need to regenerate Makefile.in, you will need Automake 1.11 or
  later.  For bootstrap or if you change configure.ac or any of the m4
  files it includes and need to regenerate configure or config.h.in, you
  will need Autoconf 2.64 or later.


BUILDING

  You can build codon-optimizer with:

      ./configure
      make

  Pass --prefix=<path> to specify <path> as the root install directory.

  If using a version from the git repository, bootstrap the build system
  with:
  
     ./autogen


USING THIS CODE

  The program assumes input sequence files are in FASTA format.  After
  building the software, command line options and usage can be determined
  with:

      ./codon-optimizer
  
  At present, the usage is:

      Usage: codon-optimizer [options] <fasta_file>
      
      Allowed options:
      
      Generic:
        -h [ --help ]         produce this help message
      
      Design Specifications:
        -s [ --start-index ] arg (=1)     first index in FASTA file of sequences to 
                                          optimize
        -e [ --end-index ] arg (=1)       last index in FASTA file of sequences to 
                                          optimize
        -f [ --forbidden-motif-file ] arg a newline separated file containing 
                                          forbidden motifs
        -d [ --desired-motif-file ] arg   a newline separated file containing desired
                                          motifs
      
      Other:
        -o [ --optimized-sequence-file ] arg (=optimized.fasta)
                                              Output file for optimized sequences.
        -t [ --trace-file ] arg (=optimized.trace)
                                        Trace file for optimized sequences.


HOMEPAGE

  The codon-optimizer web page is at:

      http://www.cs.ubc.ca/labs/beta/Projects/codon-optimizer

  will always have the current version of this package, the current
  documentation, and pointers to any additional resources.


  Please send any bug reports, patches, or questions to cthachuk@cs.ubc.ca.
