****************************************************************************
*                                                                          *
*    PHD: Profile fed neural network systems from HeiDelberg               *
*    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~               *
*                                                                          *
*    Prediction of:			                                   *
* 	secondary structure,   			   by PHDsec		   *
* 	solvent accessibility, 			   by PHDacc		   *
* 	and helical transmembrane regions, 	   by PHDhtm		   *
*                                                                          *
*    Author:             						   *
*	Burkhard Rost							   *
*       EMBL, 69012 Heidelberg, Germany					   *
*       Internet: Rost@EMBL-Heidelberg.DE				   *
*                                                                          *
*    All rights reserved.                                                  *
*                                                                          *
****************************************************************************
*                                                                          *
*    The network systems are described in:   	                     	   *
*                                                                          *
*    PHDsec:    B Rost & C Sander: JMB, 1993, 232, 584-599.		   *
*    		B Rost & C Sander: Proteins, 1994, 19, 55-72.		   *
*    PHDacc:  	B Rost & C Sander: Proteins, 1994, 20, 216-226.		   *
*    PHDhtm:  	B Rost et al.: 	   Prot. Science, 1995, 4, 521-533.	   *
*                                                                          *
****************************************************************************
*                                                                          *
*    Some statistics                                                       *
*    ~~~~~~~~~~~~~~~                                                       *
*                                                                          *
*    Percentage of amino acids:                                            *
*    +--------------+--------+--------+--------+--------+--------+         *
*    | AA:          |    Y   |    P   |    D   |    V   |    R   |         *
*    | % of AA:     |   11.1 |   11.1 |   11.1 |    8.3 |    8.3 |         *
*    +--------------+--------+--------+--------+--------+--------+         *
*    | AA:          |    Q   |    L   |    T   |    N   |    G   |         *
*    | % of AA:     |    8.3 |    8.3 |    5.6 |    5.6 |    5.6 |         *
*    +--------------+--------+--------+--------+--------+--------+         *
*    | AA:          |    S   |    I   |    H   |    F   |    E   |         *
*    | % of AA:     |    2.8 |    2.8 |    2.8 |    2.8 |    2.8 |         *
*    +--------------+--------+--------+--------+--------+--------+         *
*    | AA:          |    A   |                                             *
*    | % of AA:     |    2.8 |                                             *
*    +--------------+--------+                                             *
*                                                                          *
*    Percentage of helical trans-membrane predicted:                       *
*    +--------------+--------+--------+                                    *
*    | SecStr:      |    H   |    L   |                                    *
*    | % Predicted: |    0.0 |  100.0 |                                    *
*    +--------------+--------+--------+                                    *
*                                                                          *
****************************************************************************
*                                                                          *
*    PHD output for your protein                                           *
*    ~~~~~~~~~~~~~~~~~~~~~~~~~~~                                           *
*                                                                          *
*    Jury on:        4    different architectures (version   8.94_69  ).   *
*    Note: differently trained architectures, i.e., different versions can *
*    result in different predictions.                                      *
*                                                                          *
****************************************************************************
*                                                                          *
*    About the protein                                                     *
*    ~~~~~~~~~~~~~~~~~                                                     *
*                                                                          *
*    HEADER                                                                *
*    COMPND                                                                *
*    SOURCE                                                                *
*    AUTHOR                                                                *
*    SEQLENGTH    36                                                       *
*    NCHAIN        1 chain(s) in query data set                            *
*    NALIGN        2                                                       *
*    (=number of aligned sequences in HSSP file)                           *
*                                                                          *
****************************************************************************
*                                                                          *
*    WARNING                                                               *
*    ~~~~~~~                                                               *
*                                                                          *
*    Expected accuracy is about 94% if, and only if, the alignment contain *
*    sufficient information.  For your sequence there were not many        *
*    homologues in the current version of Swissprot detected.  This        *
*    implies that the expected accuracy is some percentage points lower !  *
*                                                                          *
*                                                                          *
*    protein:       query          length       36                         *
*                                                                          *
--- 
--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION: SYMBOLS
--- AA           : amino acid in one-letter code
--- PHD htm      : HTM's predicted by the PHD neural network
---                system (H=HTM, ' '=not HTM)
--- Rel htm      : Reliability index of prediction (0-9, 0 is low)
--- detail       : Neural network output in detail
--- prH htm      : 'Probability' for assigning a helical trans-
---                membrane region (HTM)
--- prL htm      : 'Probability' for assigning a non-HTM region
---          note: 'Probabilites' are scaled to the interval
---                0-9, e.g., prH=5 means, that the first 
---                output node is 0.5-0.6
--- subset       : Subset of more reliable predictions
--- SUB htm      : All residues for which the expected average
---                accuracy is > 82% (tables in header).
---          note: for this subset the following symbols are used:
---             L: is loop (for which above ' ' is used)
---           '.': means that no prediction is made for this,
---                residue as the reliability is:  Rel < 5
--- other        : predictions derived based on PHDhtm
--- PHDFhtm      : filtered prediction, i.e., too long HTM's are
---                split, too short ones are deleted
--- PHDRhtm      : refinement of neural network output 
--- PHDThtm      : topology prediction based on refined model
---                symbols used:
---             i: intra-cytoplasmic
---             T: transmembrane region
---             o: extra-cytoplasmic
--- 
--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION
                  ....,....1....,....2....,....3....,....4....,....5....,....6
         AA      |GPSQPTYPGDDAPVEDLIRFYDNLQQYLNVVTRHRY|
         PHD htm |                                    |
 detail: 
         prH htm |000000000000000000000000000000000000|
         prL htm |999999999999999999999999999999999999|
 subset: SUB htm |....................................|
--- 
--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION END
--- 
