
 FOG, A tool to map genomics features onto coding genes written in Perl
 Copyright (c) Sonika Tyagi, Queenland Institute of Medical Research 2009, 2010

    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 The use of FOG under the terms of the GNU General Public License is described in
 more detail in the HTML version of the FOG manual, included with this software.

 See the homepage for web interface of FOG at http://bioinformatics.org/webFOG


 Version release Notes:
 ----------------------

 This is the Perl source for FOG 1.0
 (c) 2009, 2010 Sonika Tyagi, Queenland Institute of Medical Research
 Sonika can be contacted via her email address: tyagisonika@bioinformatics.org

 

 Source Code Notes:
 -------------------
 
 FOG 1.0 package includes following files:

 map-features-on-genes-v1.0.pl 	perl source code file
 test.psl	an example of .psl format
 to-psl.pl	a perl script to make a dummy .psl format
 hg18-annotation.txt		Gene annotations ver hg18
 hg19-annotation.txt		Gene annotations ver hg19		
 
 Details on .psl format can be found here: http://genome.ucsc.edu/FAQ/FAQformat.html#format2 

 script 'to-psl.pl':
 --------------------

 This script accepts a 4 column format separated by tabs in the following order: "featureName chromosome start end". 
 Strand information is also used to cretae .psl format. By default it assumes '+'. If strand information 
 is also available, use 5 column format with appropriate options, in the order: "featureName chromosome strand start end". 
 Use command 'perl to-psl.pl -h' to obtain more help on the syntax to run this script.


 BLAT
 -------
 BLAT can be used to obtain genomic coordinates of features.
 1. Please download BLAT source from here:
    http://hgwdev.cse.ucsc.edu/~kent/src/.
 2. unzip the source file and use an executable file 'blat' to generate .psl output. 
    Sequence should be in FASTA format
 3. Use the following command to run blat:
    ./blat <database> <query> -t=dna -q=dna -out=psl <outputfile.psl>
`
