**************************************************
* Description of the GGsnp_update.pl PERL script *
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GGsnp_update_Help.txt file

VERSION 0.1
19 Fevrier 2003

AMILHAT Laurence, LEROY Philippe
Annotation & Cartographie In Silico
UMR INRA-UBP ASP Clermont-Ferrand
234 Avenue du Brezet, Domaine de Crouel
63 039 Clermont-Ferrand Cedex 2, France

contact : leroy@clermont.inra.fr

This PERL script as been written by Laurence AMILHAT to facilitate
the extraction of a valid FASTA file of the "Unigene" (contig consensus
sequences + singletons) using the updated data files of
the "Wheat SNP development" initiative. Then, this script should
be used only within this context.

The PERL script is normaly distributed with the updated data files at
the following address : 
http://wheat/pw.usda.gov/ITMI/2002/WheatSNP.html

The script source can also been download from :
http://wheat/pw.usda.gov/ITMI/2002/WheatSNP/software.html

To use correctly the GGsnp_update.pl script you need to have 
in the same directory :
	1. the singleton file in a fasta format
	2. The directory with all the contigs
	3. The GGsnp_update.pl PERL script

Remarks : when you unzip and untar the download files you may
	  recover other files (cultivar_* files for exemple)

	Concerning the script itself you may have to modify the first
	line of the script to indicate properly the PERL path.
	In our case the command line is as follow :
	#!/usr/local/public/bin/perl

	IN YOUR CASE THIS PATH MAY CHANGED ?

 The purpose of the script is to build a unique FASTA file with all 
 the contigs and singletons. All characters which are not A T G C or N 
 are translated in a N character (IUB codes and *)

We give here some examples of how the updated data files should be 
formated :

singletons.fasta file
=====================
>U19CA653661
GGACCAGCTTGTTGAAATCATCAAGGTCCTTGGTACCCCTACAAGGGAAGAAATTAAATG
CATGAACCCAAATTATACAGAGTTCAAATTCCCACAGATTAAAGCACACCCATGGCACAA
GGTATTCCATAAAAGGATGCCACCTGAAGCTGTTGATCTAGTCTCTCGGCTCCTCCAGTA
CTCGCCCAACCTAAGATGCACTGCTGTTGAGGCACTTGTTCACCCCTTCTTTGATGAGCT
...........

contigs Directory
=================
In the contigs directory you should have thousands of files
names contig-### each file having a different number (###).
Each contig file should start with the contig consensus sequence
following with EST sequences used to build the consensus sequence.
Each contig file is not in a FASTA format.
It is important that each contig sequence was named >contig-###

exemple
=======
>contig-9997.1
AGGCACGCTCCCGGCGCTCGAGCTCTGCTACTCCATGACCCAGCGCCTCCACCTGGTGGACGACGACAAGGACAAGCCGCCGCTGCTGCAGCAGCAGCACGAAGGCGCTGCCGCCGCACCGGATGCCTCCGCGCCGTCGCCGCCCGTCACCAACTGGAAGATCTCCAGCCCCGGTGACAGCCCGGACGAGGTGAAGGCGCGGCTCAAGTACTGGGCGCAGGCGGTGGCGTGCACCGTTCGCCTCTGCAGCTGAACGACGGCGACCATCCACGCGGCACACCATTCGCCGCCGGCAAACACACCATACTATATATCATACATGCCGCCGCCGCAGCCCGCAAGAAACGATCGCCGACGAGGACAACGAAAGAGTAAACGACGGACCAAGAAGGGACATGCCGGACGACCAGACCTCACCTGATCGCGAACGCGCTGCTGCTGCTGCTGCCGTCGTAAAGTGATGGGGGGCGTTGGCAACTGCATGCCATGATTGATTGCAGCTGGAGAGTTTGGTGGAGCGTTGTTGCTTGTTGGTAGTCGTCGGAGCAGCACACATGGGCTGGGCAGGTGGGAGGCGGTTTGGTTGGTTGGTTGCCCGAGTTGCTGTGTGCTCTTGTTCCAGCTGAGCAACCTGCGTCTCCTTAGCAGCAGTGATCAAAATAATGTGCAGAGTAATTAGTAGGACTACTGCAAATCTGGGGATCGGAGTGATTGAATGAATGAATAAATAAATCCACAGATCTCATTATGTTTGTTGCTTTCTTAATC
>CSPCA487051
AGGCACGCTCCCGGCGCTCGAGCTCTGCTACTCCATGACCCAGCGCCTCCACCTGGTGGACGACGACAAGGACAAGCCGCCGCTGCTGCAGCAGCAGCACGAAGGCGCTGCCGCCGCACCGGATGCCTCCGCGCCGTCGCCGCCCGTCACCAACTGGAAGATCTCCAGCCCCGGTGACAGCCCGGACGAGGTGAAGGCGCGGCTCAAGTACTGGGCGCAGGCGGTGGCGTGCACCGTTCGCCTCTGCAGCTGAACGACGGCGACCATCCACGCGGCACACCATTCGCCGCCGGCAAACACACCATACTATATATCATACATGCCGCCGCCGCAGCCCGCAAGAAACGATCGCCGACGAGGACAACGAAAGAGTAAACGACGGACCAAGAAGGGACATGCCGGACGACCAGACCTCACCTGATCGCGAACGCGCTGCTGCTGCTGCTGCCGTCGTAAAGTGATGGGGGGCGTTGGCAACTGCATGCCATGATTGATTGCAGCTGGAGAGTTTGGTGGAGCGTTGTTGCTTGTTGGTAGTCGTCGGAGCAGCACACATGGGCTGGGCAGGTGGGAGGCGGTTTGGTTGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>CSPCA485268
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTGACAGCCCGGACGAGGTGAAGGCGCGGCTCAAGTACTGGGCGCAGGCGGTGGCGTGCACCGTTCGCCTCTGCAGCTGAACGACGGCGACCATCCACGCGGCACACCATTCGCCGCCGGCAAACACACCATACTATATATCATACATGCCGCCGCCGCAGCCCGCAAGAAACGATCGCCGACGAGGACAACGAAAGAGTAAACGACGGACCAAGAAGGGACATGCCGGACGACCAGACCTCACCTGATCGCGAACGCG......... ect. ...