This folder contains some useful software to split a genome in FASTA format
into all potential virtual SAGE-tags.

First, the folder formater_soft contains a software to properly format a
FASTA file. This software should be used first. The file formater_soft.tar.gz
contains all files on that subfolder.

Second, the folder subseq_soft contains a software to generate all subsecuences
of a given length from an input FASTA file (which could contain multiple
sequences). This software should be used after the formater has been executed.
The file subseq_soft.tar.gz contains all files on that subfolder.

Third, the folder pattern_soft contains a software to obtain the subset of
subsequences that match a given pattern at their 5' end. This software should be
used after the other two have been successfully executed. The file pattern_soft.tar.gz
contains all files on that subfolder.

Fourth, a demo script (file script.csh) is included, which uses these software tools
to obtain all potential virtual SAGE-tags from the yeast genome after using a combination
of the NlaIII-BsmFI anchoring and tagging enzymes, respectively. To run this program properly,
first download all the relevant software described above. Then, compile each software tool.
To do that, just run 'make' in each software tool subfolder. After that, copy the executables
into the same directory where the 'script.csh' is found. Then, download into that directory the 
file 'yeast_genome.fasta.gz', which contains the full yeast genome, in a compressed format for 
a faster downloading process. Then uncompress that file by executing the following commnad on 
the shell:

gunzip yeast_genome.fasta.gz

Then, simply run the following command:

./script.csh

NOTE: You could explore the file 'script.csh', which is a text file, to see how the software
tools are executed. This software can be used with any genome.

WARNING: The software 'subseq_fr' will produce a file that uses N times more space as the original
FASTA genome file, where N is the size of the subsequences generated. Therefore, be sure that
enough hard disk space is available when running this sofware. After the 'pattern' software
has been executed, this large file can be removed from the disk.