SSR Finder README

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

Required Software for running SSR Finder:

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

Supported Operating Systems:
UNIX or UNIX-like operating systems:
  SSR Finder 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

Windows operating systems:
  SSR Finder currently uses some unix commands that should prohibit it from
  functioning on Windows-based systems.  Time and interest could result in
  a Windows-compatible version (barring the availability of the other required
  software components).
  
Macintosh operating systems:
  Not tested and not expected.
  Mac OS X may be able to run SSR Finder if the other required software is
  available.

Initial Setup

- extract the software distribution:

  gunzip -c ssrfinder_1_0.tar.gz | tar xvf -
  
- this generates a directory setup as follows:

  |-ssrfinder_1_0              # directory created by unpacking
    |-0_README                 # this readme file
    |
    |-scripts                  # the SSR Finder Perl scripts
    |  |-1_ssr_repeat_finder.pl
    |  |-2_ssr_primer_design.pl
    |  |-3_ssr_primer_rep_check.pl
    |  |-4_ssr_primer_blast.pl
    |  |-5_ssr_order_filter.pl
    |  |-6_ssr_order_formatter.pl
    |
    |-db                       # location of the BLAST databases
    |  |-AllPrimers.nt
    |
    \-20030101                 # example working directory
      |-repeats                # needed working subdirectory
      |
      \-CheckedIDs.txt         # list of previously checked sequences


- 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 of
  SSR Finder.

- Create a directory under this working directory named 'repeats'.
  4_ssr_primer_blast.pl will place FASTA formatted files in 'repeats'
  for BLAST comparison.

- Create a file listing all the sequence ids/names that have been previously
  checked for repeats (this prevents rechecking sequences when a periodic
  species specific retrieval is done from GenBank for instance).
  This file is named 'CheckedIDs.txt'
  If you are starting from scratch you can simply use an empty file:
  touch CheckedIDs.txt
  
  After running '1_ssr_repeat_finder.pl' a file named 'new_ids<datename>.txt'
  is created which can be appended to CheckedIDs.txt for subsequent runs.
  
- Prepare a BLAST database for holding primer sequences for checking
  to start with an empty database do the following:
  from the ssrfinder_1_0 directory run the following commands:

    touch db/AllPrimers.nt
    formatdb -i db/AllPrimers.nt -p F -o T

  to start with a set of sequences/primers that you have previously generated
  (so that you do duplicate previous work) do the following:
  copy your sequences (FASTA format) into the file:
    ssrfinder_1_0/db/AllPrimers.nt
  from the ssrfinder_1_0 directory run the following commands:

    formatdb -i db/AllPrimers.nt -p F -o T

- Sequences to be searched should be in fasta format and the file named
  'sequence<datename>.txt'.
  Where <datename> corresponds to the working directory and is set in 
  each of the Perl scripts.

- Edit the parameters specified at the begining of each of the 6 Perl scripts
  to reflect the current job.


Order of execution:

1_ssr_repeat_finder.pl
2_ssr_primer_design.pl
3_ssr_primer_rep_check.pl
4_ssr_primer_blast.pl
5_ssr_order_filter.pl
6_ssr_order_formatter.pl

INPUT FILE descriptions:

       sequence<datename>.txt  - Input sequence file in fasta format 
               CheckedIDs.txt  - The list of IDs that have already been
                                 searched for repeats 

OUTPUT FILE descriptions:

       labdbout<datename>.txt  - The output file for for loading data
                                 into MMP-LIMS 
         ssrout<datename>.txt  - The output file for the SSR results 
        new_ids<datename>.txt  - The output file for the sequence ids 

     raw_primer<datename>.out  - Resulting raw primer3 output from the
                                 ssr_finder script 
 primer_results<datename>.txt  - Resulting primers from the ssr_finder
                                 script 

     rescreened<datename>.txt  - List of valid primers plus flanking
                                 sequence

fullblastoutput<datename>.txt  - Formatted output from BLAST alignment
       blastout<datename>.txt  - The output file for the BLAST results 

         filter<datename>.txt  - List of primers with no BLAST hits  

          order<datename>.txt  - List of primers along with information
                                 helpful for ordering primers

OTHER FILES

                 primerin.txt  - Input file for Primer3 generated by
                                 the script

Contact Information:

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

 - Steven Schroeder <SchroederSG@missouri.edu>