PoSSuM - Fast and Sensitive Matching of Position Specific Scoring Matrices
Using Enhanced Suffix Arrays
Version 1.3 (August 2007)


o About this software...
	PoSSuM contains implementations of the ESAsearch and LazyDistrib 
	algorithms described in:
  
	M. Beckstette, D. Strothmann, R. Homann, R. Giegerich, S. Kurtz; 
	Fast and Sensitive Matching of Position Specific Scoring Matrices 
	using Enhanced Suffix Arrays, Proc. German Conference on 
	Bioinformatics, 2004, GI-Edition, Lecture Notes in Informatics, 
	volume P-53, pages 53-64
	
	The included mkvtree program for the generation of the index is taken
	from the VMATCH package (see: http://www.vmatch.de) written by Stefan
	Kurtz.

	Basically you give PoSSuM an enhanced suffix array of your 
	sequences, built with mkvtree, a collection of position specific 
	scoring matrices and a threshold as input; it will return all 
	matches of the specified PSSMs on the provided sequences.

o Files included in this package are
	bin/possumsearch
	bin/possumsearch-mt
	bin/possumdist
	bin/possumdist-mt
	bin/possumfreqs
	bin/prints2gen
	bin/transfac2gen
	bin/mkvtree
	share/PoSSuM/doc/README
	share/PoSSuM/doc/license.txt
	share/PoSSuM/examples/demo.fas
	share/PoSSuM/examples/demo.lib
	share/PoSSuM/examples/demo.sh
	share/PoSSuM/examples/results.txt

	Optionally: a PDF and/or PS containing the PoSSuM user manual in
	            share/PoSSuM/doc/.

o Getting PoSSuM
	WWW home: http://bibiserv.techfak.uni-bielefeld.de/possumsearch/

o Using PoSSuM
	See the manual file PoSSuM-1_3.pdf for detailed instructions.

o Getting started with PoSSuM
	See the demo file demo.sh in the examples directory for a quick
	introduction to how to use the programs of the PoSSuM package.

o Reporting bugs
	These programs are under active development. Though this
	release has been tested and appears to be stable, bugs may crop up. 
	Please report suggestions, comments, and bug reports to
	rhomann@techfak.uni-bielefeld.de


Michael Beckstette (mbeckste@techfak.uni-bielefeld.de)


Dipl.-Inform. Michael Beckstette
AG-PI / Technische Fakultaet
Universitaet Bielefeld
Postfach 100131
D-33501 BIELEFELD
Germany
