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  1. summary This describes the basic usage of this software

Building

The included Makefile should be all that is needed to build this software. A working OpenMP implementation is required, as well as the gcc compiler. Simply type "make" in the code directory.

Running

After building the software, the user may run it, using these parameters: 

  * -f filename (this is the input file name in FASTA format)
  * -L parameterval (this is the L parameter as described in the papers)
  * -W parameterval (this is the W parameter as described in the papers)
  * -K parameterval (this is the K parameter as described in the papers)
  * -v version (this can be either "seq" or "occ" depending on preference)

For instance, here is a sample configuration:

Papers

The following publications describe the algorithm in detail: 

  * Rigoutsos, I. and A. Floratos, Combinatorial Pattern Discovery in Biological Sequences: the TEIRESIAS Algorithm. Bioinformatics, 14(1), January 1998.


  * Rigoutsos, I. and A. Floratos. Motif Discovery Without Alignment Or Enumeration. Proceedings 2nd Annual ACM International Conference on Computational Molecular Biology (RECOMB '98), New York, NY. March 1998.