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ensemble_alignment
example
facet
gnu/getopt
psipred_scripts
v1.1
v1.3
v1.4
.classpath
.gitignore
.project
FACET_v1.4.tgz
README
runFACET.sh

README

***************************
*      FACET v1.4         *
*                         *
*     release date        *
*     8 August 2015       *
***************************

For details on this algorithm see Kececioglu and DeBlasio 2013 (Journal of Computational Biology). And see http://facet.cs.arizona.edu for more examples and psipred conversion scripts.

FACET (Feature-based Accuracy Estimator) can be run simply using the following command:

     ./runFACET.sh <seq> <struc> <prob>

Where the variables are as follows:

<seq> - the path to a sequence file in FASTA format of n sequcnes

<struc> - is the unaligned sequence structure predictions from psipred32 (not included)
	this file should be n lines long

<prob> - the unaligned sequence structure class predictions from psipred32 (not included)
	should contain 3*n lines
	
	
MODIFICATION
------------
The Facet executable comes loaded with the coefficients from Kececioglu and DeBlasio 2013.  
The polynomial function can be modified in Facet.java.  The package was built to be included 
in other applications written in java.


STRUCTURE
---------

sequence structure predictions should be made using psipred32, you can install psipred by 
using these instructions:

(1) Get psipred, e.g.
$ mkdir psipred32
$ cd psipred32
$ wget http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/psipred32.tar.gz
$ tar -xzf psipred32.tar.gz
$ cd src
$ make

(2) Open the psipred script runpsipred (in the psipred installation
directory), and modify all locations lines that need to be modified.

(3) move into the psipred_scripts folder and update the pripred 
location and temporary work space for the psipred output files.
(on lines 5, update the values of $TEMP_FILE_LOCATION)

(4) run ./psipred_wblast.pl on the input fasta file as follows:

	./psipred_wblast.pl <seq> > <struc> 2> <prob>


(note that you can use ./psipred.pl and runspipred_single, but the preiction results might be varried.)

MODIFICATION
------------
v1.0 :	Initial Release (March 2013)
v1.1 :	Updated to make Facet work correctly when downloaded in alternate regions (January 2014)
v1.3 :  Found a small error when calculating blockiness when ignoring gaps in block columns, previous version over counted aligned pairs.
v1.4 :  Added ensemble alignment scripts with thier own README, added the ability to define coefficients from the command line when calling Java directly