CMfinder 0.2.2
============
   October 2010
   Updated to include pscore and weighted ranking
   (seemann@rth.dk)

   March 2006
   The last public version of this package can be found at
  
   http://bio.cs.washington.edu/yzizhen/CMfinder


Content
=======

1. Terms of use
2. Introduction
3. Installation
4. Citing CMfinder
5. Usage
7. Contact
8. Credits


1. Terms of use
===============
The files in the directory "cmfinder" and scripts in "bin" are
copyright 2006 by Zizhen Yao, except where otherwise noted.  
The entire package CMfinder uses many codes developed by others, and is
distributed under the GNU General Public License. 

Refer to COPYRIGHT and LICENSE for licence terms of CMfinder.


2. Introduction 
=============== 
CMfinder is a RNA motif prediction tool. It is an expectation
maximization algorithm using covariance models for motif description,
carefully crafted heuristics for effective motif search, and a novel
Bayesian framework for structure prediction combining folding energy
and sequence covariation. This tool performs well on unaligned
sequences with long extraneous flanking regions, and in cases when the
motif is only present in a subset of sequences. CMfinder also
integrates directly with genome-scale homology search, and can be used
for automatic refinement and expansion of RNA families.

3. Citing CMfinder 
================== 
Zizhen Yao, Zasha Weinberg, and
Walter L. Ruzzo.  CMfinder--a covariance model based RNA motif finding
algorithm.  Binformatics, 2006 22: p. 445-452.


4. Installation 
=============== 
First unpack the .tgz file, and "make".

% tar xfz cmfinder-0.2.2.tgz
% cd CMfinder_0.2.2 
% make

Then get wublast package from (http://blast.wustl.edu/licensing/),
and install it. Make sure that the installed binary programs 
contain "blastn" and "xdformat". You can run CMfinder without the BLAST, 
but with potential performance loss.

Finally add CMfinder-0.2/bin to your PATH, and set Environment
variables: For csh, add the following to your .cshrc file
   set PATH = ($PATH, your_cmfinder_bin_path)
   setenv CMfinder your_cmfinder_bin_path
   setenv BLAST your_blast_path

for bash, add the following to your .bash file
   export PATH=$PATH:your_cmfinder_bin_path
   export CMfinder=your_cmfinder_bin_path
   export BLAST=your_blast_path

CMfinder and dependent packages are written in C, and should be easily
portable.  It is still a preliminary version, and tested mainly on Linux 
(and very lightly on Mac OS X).
 

5. Usage 
========

See USERGUIDE for details.


6. Contact 
==========

Please feel free to contact the author for bug-reports,
feature-requests, suggestions etc.

Zizhen Yao <yzizhen@cs.washington.edu>

7. Credits 
========== 
CMfinder is written by Zizhen Yao from Larry
Ruzzo's lab at University of Washington, Seattle.  
Many thanks to Zasha Weinberg and Larry Ruzzo for
contributing great ideas and feedbadk during the 
development.

CMfinder uses many codes developed by others:

The "infernal", "squid", "easel" code are taken from Infernal 0.7
(http://www.genetics.wustl.edu/eddy/infernal/)
developed by Dr Sean Eddy's lab at Washington University in
St. Louis. Our intial version (CMfinder 0.1) used Infernal 0.55.

Two files - "automaker.c", "cmfinder.c" under "cmfinder"
directory also used some code from COVE 
(http://selab.wustl.edu/cgi-bin/selab.pl?mode=software#cove),
also developed by Dr Sean Eddy's lab at Washington University 
in St. Louis.

The "vienna" is derived from Vienna RNA package 1.5
(http://www.tbi.univie.ac.at/~ivo/RNA/) developed by Ivo
Hofacker et al. at Institut fr theoretische Chemie.

See the corresponding subdirectories for further details, including 
license information.
