dSNP Primer Designer README

author:      Steven Schroeder <SchroederSG@missouri.edu>
institution: University of Missouri-Columbia, Maize Mapping Project
date:        2003-01-01

Required Software for running dSNP Primer Designer:

Perl *NOTE: the first line of the included perl scripts may need to be altered
            to reflect the local install of Perl
Primer3

Supported Operating Systems:
UNIX or UNIX-like operating systems:
  dSNP Primer Designer should run without problems on most UNIX or UNIX-like 
  operating systems

  Known to work:
  Solaris 7, Solaris 8
  FreeBSD 4.X, FreeBSD 5.0

Initial Setup

- extract the software distribution:

  gunzip -c dSNPprimerdesign_1_0.tar.gz | tar xvf -
- this generates a directory setup as follows:

  |-dSNPprimerdesign_1_0       # directory created by unpacking
    |-0_README                 # this readme file
    |
    |-scripts                  # the dSNP Primer Designer Perl scripts
    |  |-dSNP_primer_designer.pl
    |
    \-20030101                 # example working directory
      |
      \-sequence<datename>.fasta  # sequences to design primers from


- Create a working directory based on the date (can also be some other label)
- All scripts will reference this working directory based off the $datename
  variable which needs to be altered in each script as of this version.

- the location of the primer3 executable needs to be set near the top of the
  dSNP_primer_designer.pl script.
  
- several other variables can be adjusted as needed
  $offset_three  : location in from the 3' end of the source sequence (usually a
                   unigene) that the right hand primer should sit
  $amp_size      : sets the size of the target amplification product

Order of execution:

 dSNP_primer_designer.pl

Contact Information:

For assistance with installation and configuration or suggestions
please contact the author.

 - Steven Schroeder <SchroederSG@missouri.edu>