SHUSTRING - Compute Shortes Unique Substrings
by Bernhard Haubold and Thomas Wiehe

Unpacking and Compiling
tar -xzvf shustring_xxx.tgz
cd Shustring_xxx
make
./shustring -h

Here are a number of example commands using as input the genome of
Mycoplasma genitalium, which is part of the example data package distributed
from the same web site as the shustring software.

1) Get options:
./shustring -h

2) Print global shustrings:
./shustring < mgGenome.fasta

3) Include reverse strand in computation:
./shustring -r < mgGenome.fasta

4) Supress printing of sequence information:
./shustring -r -q < mgGenome.fasta

5) Print local shustrings for all the input sequences whose header matches the
   regular expression submitted to -l (this may take a while...):
./shustring -r -l . < mgGenome.fasta

6) Grab the header line of the previous run for a summary of the shustring
   lengths found
./shustring -r -l . < mgGenome.fasta | head

7) Print the positions of local shustrings with lengths ranging from 100 to 200:
./shustring -r -l . -q -m 100 -M 200 < mgGenome.fasta

REFERENCE
@Article{	  hau05:gen,
  author	= {Haubold, B. and Pierstorff, N. and M\"oller, F. and Wiehe,
		  T.},
  title		= {Genome Comparison without Alignment Using Shortest Unique
		  Subsequences},
  journal	= {BMC Bioinformatics},
  year		= 2005,
  volume	= 6,
  pages		= 123
}