PoSSuM - Fast and Sensitive Matching of Position Specific Scoring Matrices
Using Enhanced Suffix Arrays
Version 2.0 (June 2009)


o About this software...
	PoSSuM contains implementations of the ESAsearch and LazyDistrib 
	algorithms described in:

	M. Beckstette, R. Homann, R. Giegerich, S. Kurtz; 
	Fast index based algorithms and software for matching position
	specific scoring matrices. BMC Bioinformatics, 7:389, 2006.

	Basically, you give PoSSuM an enhanced suffix array of your sequences,
	built with mkESA (http://bibiserv.techfak.uni-bielefeld.de/mkesa/)
	or mkvtree (http://www.vmatch.de/), 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/possumdist
	bin/possumfreqs
	bin/psfamsearch.pl
	share/PoSSuM/doc/README
	share/PoSSuM/doc/license.txt
	share/PoSSuM/examples/demo.fas
	share/PoSSuM/examples/demo.lib
	share/PoSSuM/examples/demo_mkesa.sh
	share/PoSSuM/examples/demo_mkvtree.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-2_0.pdf for detailed instructions.

o Getting started with PoSSuM
	See the demo files demo_mkesa.sh and demo_mkvtree.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
