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The plant prediction function

Contact:
Birgit Eisenhaber (IMP/Austria)
Michael Wildpaner (IMP/Austria)
Frank Eisenhaber (IMP/Austria)
Carolyn Schultz (University of Adelaide/Australia)
Paul Dupree and Georg Borner (University of Cambridge/UK)

# ------------------------------------------------------------------- #
# 
# package *-> plants <-*
# *******************************
# 
# name of executable           : plants
# time of program compilation  : Oct 11 2002 (15:53:39)
# time of program execution    : Thu Oct 24 10:14:53 2002
# version of the code          : Revision: 2.1 (Date: 2002/04/05 15:38:48)
# 
ReadAapLib: AAProperty library  opened
Number of entrys in AapLib: <682>
-->All selects were switched on.


Selection parameters:
---------------------
0:     PToken: OC   
       SToken: 
         RExp: VIRIDIPLANTAE
    is_SToken: 0
       expect: 1

-->OpenSWFile: Data file <./gpi.learn.sav> opened


-->begin GPI-site evaluations
-->ReadGPILib: GPI library  opened
 INFO> ReadGPILib: VARSPLIC line in entry  .!!
 INFO> ReadGPILib: VARSPLIC line in entry  .!!
 INFO> ReadGPILib: VARSPLIC line in entry  .!!
 INFO> ReadGPILib: VARSPLIC line in entry  .!!
 INFO> ReadGPILib: VARSPLIC line in entry  .!!
 INFO> ReadGPILib: VARSPLIC line in entry  .!!
 INFO> ReadGPILib: VARSPLIC line in entry  .!!
 INFO> ReadGPILib: VARSPLIC line in entry  .!!
number of entries of file 1                   :   388
number of accepted entries of file 1          :   388
total number of entries                       :   388

-->Statistic_confidence of GPILib 1 : 
number of accepted entries                    :   388
number of entries with certain GPI-site       :    86
number of entries with potential GPI-site     :   238
number of entries with GPI-site by similarity :    64

-->GPIStatistic_Length: GPILibNumber = 1
Lmin                :  14 ( entry: PAG1_TRYBB, file: 1 )
Lmax                :  32 ( entry: T06041, file: 1 )
deltaL              :   5
number of intervals :   4
interval of length   from     to    number of entries
                 1     14     19                   25
                 2     20     24                  183
                 3     25     29                  151
                 4     30     34                   29
total number of entries                       :   388

-->Statistic_taxonomy of GPILib 1 / total number of entries 388
     1 VIRUSES
   168 EUKARYOTA
   120 ..METAZOA
     5 ....INSECTA
   113 ....VERTEBRATA
     3 ......PISCES
     5 ......AVES
   105 ......MAMMALIA
    55 ........PRIMATES
    10 ..FUNGI
    38 ..PROTOZOA
   219 ..Viridiplantae

-->degree of the polynom for fitting: 6
-->Calc_EVD_Param_PolyFit: file of values  opened
SSerr =       12.24452810
The 7 polynomial coefficients (starting from the lowest power on) are:
beta[0] = -7.608233e+00
beta[1] = -3.064603e-01
beta[2] = -6.636068e-03
beta[3] = -9.337898e-05
beta[4] = -7.492552e-07
beta[5] = -3.064883e-09
beta[6] = -4.928117e-12

Thresholds for GPI-anchor selecting:
   P-site: score =   2.00  p = 2.616277e-04
   S-site: score =  -2.00  p = 8.924251e-04
-->All flags were switched on.

-->Switch_Off_Tax: number of entries before procedure : 388
-->Flags of all entries except Viridiplantae switched off
-->Switch_Off_Tax: number of entries after procedure : 219

-->Switch_Off_Len: number of entries before procedure : 219
-->Flags of all entries with AALen-GPIPos > 32 switched off
-->Flags of all entries with AALen-GPIPos < 17 switched off
-->Switch_Off_Len: number of entries after procedure : 219

possible largest subset found: Q =  215
possible largest subset found: Q =  199
possible largest subset found: Q =  179
largest subset found: q = 179
number of 0's in found largest subset: 0
-->Mean and Dispersion of property NAKH920105 from -11 to -1
   Mean: 5.160518
   Dispersion: 1.620981
-->Mean and Dispersion of property NAKH920105 from 3 to 8
   Mean: 6.754227
   Dispersion: 2.293874
-->Mean and Dispersion of property NAKH920105 from 10 to Sequence C-end
   Mean: 12.352371
   Dispersion: 1.574704
-->Mean and Dispersion of property NAKH920105 from 26 to Sequence C-end
   Mean: 12.438834
   Dispersion: 2.486604
-->Mean and Dispersion of property HAGECH94_V from 3 to 8
   Mean: 128.081006
   Dispersion: 17.788892
-->Mean and Dispersion of property  at position(s) -1 0 1 2 
   number of selected entries: 179
   Mean : 387.924581
   Dispersion:  42.590177
-->Mean and Dispersion of property  at position(s) -1 1 2 
   number of selected entries: 179
   Mean : 295.101117
   Dispersion:  35.890074
-->Mean and Dispersion of property  at position(s) -1 1 
   number of selected entries: 179
   Mean : 204.563128
   Dispersion:  34.443513
-->Mean and Dispersion of property  at position(s) -1 2 
   number of selected entries: 179
   Mean : 203.845251
   Dispersion:  33.012402
-->All flags were switched on.

-->Switch_Off_Tax: number of entries before procedure : 388
-->Flags of all entries except Viridiplantae switched off
-->Switch_Off_Tax: number of entries after procedure : 219

-->Switch_Off_Len: number of entries before procedure : 219
-->Flags of all entries with AALen-GPIPos > 32 switched off
-->Flags of all entries with AALen-GPIPos < 17 switched off
-->Switch_Off_Len: number of entries after procedure : 219

NSubFam = 88
Profile:
Ala
  0.4   0.1   0.3  -0.1   0.6   0.4   0.4   0.2   0.7   0.7   0.7   0.5   0.1   0.1   0.2 
  0.3   1.6   1.7   0.4   0.4   0.3   0.6   0.7   0.8   0.0   0.8   0.5   0.2   1.1   0.8 
  1.0   1.0   0.9   0.9   0.8   0.8   0.8   0.5   0.8   0.3   0.3 
Cys
  0.3   0.5   0.4   0.0  -0.2   0.3  -0.7  -1.3  -3.1  -0.6  -1.3  -0.6  -2.5  -1.3  -4.6 
 -6.1  -5.5  -1.3  -1.3   0.3  -0.9   0.0  -0.2  -0.6   0.1  -0.2  -0.6  -0.2  -1.3  -0.2 
  0.5  -0.2  -1.3  -0.2   0.6  -1.3   0.1  -0.5  -1.1  -0.3  -0.7 
Asp
  0.7   0.3   0.1   0.1  -0.2   0.1  -0.1   0.2   0.3   0.3  -0.4  -0.8   0.2  -0.4  -0.8 
  0.1  -0.5  -1.6  -1.0  -2.4  -1.3  -1.3  -4.5  -1.7  -1.7  -4.8  -2.4  -4.9  -4.5  -5.2 
 -5.0  -2.4  -5.7  -5.4  -5.0  -5.1  -5.1  -4.6  -2.2  -2.0  -4.3 
Glu
 -0.3  -0.2  -0.6  -1.0  -0.2  -0.6  -1.2  -0.7  -1.2  -1.4  -0.0  -0.4  -0.5  -0.9  -0.5 
 -6.1  -1.8  -5.7  -0.8  -0.8  -1.9  -2.6  -4.5  -1.4  -3.8  -4.8  -4.9  -4.9  -2.5  -5.2 
 -5.0  -5.3  -5.7  -5.4  -5.0  -5.1  -5.1  -4.6  -3.6  -4.4  -4.3 
Phe
 -0.3  -1.0  -0.5  -1.0  -0.7  -1.0  -0.2  -0.5  -0.7  -0.5  -1.0  -1.4  -1.0  -0.5  -2.1 
 -6.1  -2.1  -5.7  -0.2  -2.1   0.2  -0.0   0.3   0.7   0.9   0.8   0.6   0.7   0.7   0.6 
  0.1   0.6   0.7   0.7   0.6   1.4   1.5   1.2   1.1   0.9   1.3 
Gly
  0.3   0.5   0.6   0.6   0.4   0.4   0.4   0.2   0.2   0.3  -0.2   0.1   0.2  -0.4   0.6 
  0.9   1.1   1.1   0.4   0.1   0.2   0.5  -0.1   0.5   0.5   0.3   0.5   0.1  -0.3  -0.7 
 -0.0  -0.2  -0.1  -0.2  -0.6  -0.2  -0.2  -1.9  -0.7  -0.5  -0.7 
His
 -0.1  -0.1  -0.8  -0.4  -2.7  -1.5  -2.7  -0.4   0.1   0.0  -1.5  -1.5   0.3  -0.4  -0.4 
 -6.1  -5.5  -5.7   0.6  -0.2  -0.4   0.3  -0.1  -0.1  -0.1  -4.8  -1.5  -1.5  -0.8  -5.2 
 -0.8  -5.3  -5.7  -1.5  -0.8  -1.5  -5.1  -0.3  -1.3   0.8   0.5 
Ile
 -0.8  -0.5  -0.7  -0.9  -1.1  -0.7  -2.5  -0.5  -1.8  -1.1  -1.7  -0.8  -1.1  -0.8  -1.0 
 -6.1  -5.5  -5.7  -0.8  -0.7   0.0  -0.5  -0.3  -1.1   0.2  -0.8  -0.2   0.2   0.1   0.3 
 -0.6  -0.2   0.4  -0.1   0.3  -0.0   0.2  -0.3   0.3   0.2   0.2 
Lys
 -0.3  -0.7  -0.5  -0.2  -0.1  -0.8  -0.1  -0.5  -0.8  -0.6  -0.7  -0.3   0.0   0.2  -0.2 
 -6.1  -5.5  -5.7  -0.5  -0.1  -0.6  -0.1  -0.8  -1.2  -1.1  -1.8  -1.1  -2.5  -4.5  -5.2 
 -2.5  -5.3  -5.7  -5.4  -5.0  -1.4  -1.8  -2.4  -2.3  -4.4  -1.9 
Leu
 -1.2  -0.9  -0.5  -0.7  -1.2  -1.4  -1.2  -1.2  -1.0  -1.6  -1.0  -0.9  -1.0  -0.5  -4.6 
 -6.1  -5.5  -5.7  -0.6   0.0   0.2  -0.7  -0.7  -0.5   0.3   0.8   1.0   0.8   1.0   1.2 
  0.9   1.0   1.1   1.1   0.9   1.1   1.1   1.3   1.3   1.3   0.9 
Met
 -0.6  -0.6  -2.9  -0.3   0.1  -0.1  -1.7  -0.3  -1.0  -0.3  -0.9  -0.6  -0.6  -1.0  -4.6 
 -6.1  -5.5  -5.7   0.3   0.1  -0.3   0.1   0.1  -1.0  -0.3  -1.0  -0.3  -0.1  -0.0  -0.3 
  0.4   0.4   0.4   0.7   0.8   0.3  -0.2  -0.2  -0.4   0.1   0.8 
Asn
 -0.8   0.5  -0.3  -0.3  -0.3  -0.4  -0.1  -0.3  -0.2  -1.5  -0.1  -0.0  -0.6  -0.8   0.4 
  1.2  -1.5  -1.1  -0.1  -0.0  -0.0   0.4  -0.4   0.1  -0.6  -4.8  -4.9  -4.9  -1.5  -2.2 
 -5.0  -0.8  -5.7  -5.4  -5.0  -5.1  -2.2  -4.6  -1.3  -1.8  -1.6 
Pro
  1.0   1.1   0.8   1.0   1.1   1.2   1.2   1.4   0.9   1.4   1.4   1.2   1.2   1.3   1.2 
 -6.1  -1.0  -1.6   0.1   0.0   0.1  -0.6   0.5  -0.1  -0.0   0.2  -0.5  -0.4  -1.2  -2.3 
 -0.7  -0.3  -5.7  -2.3  -1.2  -5.1  -1.6  -1.1  -1.4  -4.4  -4.3 
Gln
 -0.3  -1.4  -0.3  -0.5  -0.2   0.0  -0.5  -0.2  -0.4  -0.2   0.2   0.4  -1.0  -0.4  -1.4 
 -6.1  -1.0  -2.1  -1.0  -1.0  -1.4  -1.4  -0.2  -1.0  -0.2  -2.1  -4.9  -4.9  -2.1  -2.1 
 -1.4  -5.3  -5.7  -5.4  -1.4  -5.1  -5.1  -2.0  -0.8  -1.1  -4.3 
Arg
 -1.4  -0.6  -0.6  -0.9  -0.6  -0.6  -2.5  -1.1  -0.5  -0.9  -0.4  -0.6  -0.7  -0.7  -1.1 
 -6.1  -5.5  -5.7   0.2   0.4   0.3   0.4   0.0   0.1  -0.2  -2.5  -4.9  -1.8  -2.5  -5.2 
 -5.0  -5.3  -5.7  -5.4  -2.5  -2.5  -5.1  -1.0  -2.3  -0.1  -1.2 
Ser
  0.7   0.9   0.7   0.8   0.6   0.4   0.9   0.7   0.6   0.7   0.5   0.9   0.8   0.9   1.2 
  2.0   1.5   1.2   0.9   1.0   0.6   0.6   0.7   0.8   0.6   0.1   0.5   0.3   0.2   0.4 
  0.2  -0.6  -0.3   0.1   0.1  -0.0  -0.0  -0.1   0.0  -0.4   0.5 
Thr
  0.3  -0.3   0.5   0.5   0.2   0.4   0.6   0.0   0.6   0.0   0.5   0.2   0.4   0.7   0.6 
 -6.1  -1.4  -0.1   0.3   0.4   0.1  -0.0   0.3  -0.1  -0.2  -0.0  -0.2  -0.0  -0.7  -0.5 
 -0.3  -0.4  -0.4  -0.5  -0.7  -0.6  -1.8  -1.7  -2.3  -0.7  -1.2 
Val
 -1.0  -0.8  -0.5  -0.4  -0.7  -0.6  -0.3  -0.3  -0.0  -0.7  -1.5  -1.2  -0.4  -0.7  -1.0 
 -6.1  -1.5  -1.2  -0.4  -0.7   0.5   0.1   0.3  -0.1   0.1   0.8   0.6   1.1   0.6   0.9 
  0.9   0.9   1.0   0.8   0.9   0.4   0.5   0.8  -0.1  -0.1   0.6 
Trp
 -2.2  -1.0  -1.1  -2.3  -0.3  -1.0  -1.0  -1.0  -3.1  -2.2  -1.0  -2.2   0.5  -1.0  -4.6 
 -6.1  -5.5  -5.7  -0.4  -1.1  -1.0  -0.4  -4.5   0.4   0.4   0.8  -1.0   0.7  -4.5  -5.2 
 -0.3  -0.4  -5.7  -0.3  -0.3  -0.3  -0.3  -0.2   0.8   0.6  -0.4 
Tyr
 -0.3  -1.2  -1.9  -0.2  -0.5   0.2  -0.8  -0.3  -0.8  -0.3   0.3  -0.3  -0.8  -0.1  -1.2 
 -6.1  -5.5  -5.7  -0.5  -1.9  -1.2  -1.2  -0.5  -0.3  -0.1  -1.2  -1.2  -0.8  -1.9  -1.9 
 -1.9  -5.3  -5.7  -1.9  -0.3  -0.3  -1.8  -0.4  -0.6  -0.4  -0.2 

ConsensSequence: p s s s a p s p a p p s p p s S a a s s s a a a l l l l l l l l l l l l l l l l l

Positions with profile component > 1.0 for all amino acid types
Ala  1 2 13
Cys 
Asp 
Glu 
Phe  20 21 22 23 25
Gly  1 2
His 
Ile 
Lys 
Leu  14 16 17 18 20 21 22 23 24
Met 
Asn  0
Pro  -15 -14 -12 -11 -10 -9 -8 -6 -5 -4 -3 -2 -1
Gln 
Arg 
Ser  -1 0 1 2 4
Thr 
Val  12
Trp 
Tyr 

Parameters for score calculation:
---------------------------------
TaxonCode: 10000
Calculation of profile:
   number of input sequences: 219
   number of regions: 5
   1: from                :  -15
      to                  :  -12
      weight of region    :  0.0
   2: from                :  -11
      to                  :   -2
      weight of region    :  0.5
   3: from                :   -1
      to                  :    2
      weight of region    :  3.0
   4: from                :    3
      to                  :    9
      weight of region    :  0.5
   5: from                :   10
      to                  :   25
      weight of region    :  1.0
   weight of profile      :  0.6
omega-site will be searched in interval [12..40] from C-terminal

Function 0 = Combi_contents_win_penalty : contents and windows of DE in N-terminal region
   Parameters:
   ScFunc[0].from         =           -11
   ScFunc[0].to           =            -1
   ScFunc[0].PropertyName =            DE sections
   ScFunc[0].par1         =         -4.00 penalty
   ScFunc[0].par2         =         50.00 threshold: percentage of DE in N-terminal region
   ScFunc[0].par4         =             3 winlen
   ScFunc[0].par5         =             2 par5 DEs are max allowed per window if par2 is exceeded
   ScFunc[0].wfunc        =          1.00
Function 1 = Lower_Average : hydrophilicity of N-terminal region [-11..-1]
   Parameters:
   ScFunc[1].from         =           -11
   ScFunc[1].to           =            -1
   ScFunc[1].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[1].par1         =          5.16 mean hydrophobicity for N-terminal region was calculated
   ScFunc[1].par2         =          1.62 dispersion was calculated
   ScFunc[1].wfunc        =          1.00
   ScFunc[1].distr_type   =       F_GAUSS

Function 2 = PenaltyForBadProfile : penalty for bad Omega-Site
   Parameters:
   ScFunc[2].from         =             0
   ScFunc[2].to           =             2
   ScFunc[2].par1         =          0.10 threshold
   ScFunc[2].par2         =         -4.00 penalty
   ScFunc[2].wfunc        =          1.00

Function 3 = Sum : volume function
   Parameters:
   ScFunc[3].from         =            -1
   ScFunc[3].to           =             2
   ScFunc[3].PropertyName =    HAGECH94_V mean volume of residues
   ScFunc[3].par1         =        387.92 mean volume was calculated
   ScFunc[3].par2         =         42.59 dispersion was calculated
   ScFunc[3].wfunc        =          1.00
   ScFunc[3].distr_type   =       F_GAUSS

Function 4 = Sum3 : volume function for three positions
   Parameters:
   ScFunc[4].from         =            -1 Position 1
   ScFunc[4].to           =             2 Position 2
   ScFunc[4].PropertyName =    HAGECH94_V mean volume of residues
   ScFunc[4].par1         =        295.10 mean volume was calculated
   ScFunc[4].par2         =         35.89 dispersion was calculated
   ScFunc[4].par4         =             1 Position 3
   ScFunc[4].wfunc        =          1.00
   ScFunc[4].distr_type   =       F_GAUSS

Function 5 = Sum2 : volume function for two positions
   Parameters:
   ScFunc[5].from         =            -1 Position 1
   ScFunc[5].to           =             1 Position 2
   ScFunc[5].PropertyName =    HAGECH94_V mean volume of residues
   ScFunc[5].par1         =        204.56 mean volume was calculated
   ScFunc[5].par2         =         34.44 dispersion was calculated
   ScFunc[5].wfunc        =          0.50
   ScFunc[5].distr_type   =       F_GAUSS

Function 6 = Penalty_Mobility : penalty for more than one residue out of P, T, V, I
   Parameters:
   ScFunc[6].from         =            -1
   ScFunc[6].to           =             2
   ScFunc[6].PropertyName =          PTVI residues
   ScFunc[6].par1         =         -4.00 penalty
   ScFunc[6].wfunc        =          1.00

Function 7 = C_Position : penalty, if site is outside of interval[from..to] relative to C-terminal
   Parameters:
   ScFunc[7].from         =            17
   ScFunc[7].to           =            32
   ScFunc[7].par1         =          0.50 lambda (x < from)
   ScFunc[7].par2         =          1.00 lambda (x > to)
   ScFunc[7].wfunc        =          4.00
   ScFunc[7].distr_type   =   F_BOLTZMANN

Function 8 = Lower_Average : hydrophilicity of spacer region [3..8]
   Parameters:
   ScFunc[8].from         =             3 (after omega-site)
   ScFunc[8].to           =             8
   ScFunc[8].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[8].par1         =          6.75 mean hydrophobicity for spacer region was calculated
   ScFunc[8].par2         =          2.29 dispersion was calculated
   ScFunc[8].wfunc        =          2.00
   ScFunc[8].distr_type   =       F_GAUSS

Function 9 = Lower_Average : function for spacer volume (mean for positions 3..8)
   Parameters:
   ScFunc[9].from         =             3 (after omega-site)
   ScFunc[9].to           =             8
   ScFunc[9].PropertyName =    HAGECH94_V mean volume of residues
   ScFunc[9].par1         =        128.08 mean volume for spacer region was calculated
   ScFunc[9].par2         =         17.79 dispersion was calculated
   ScFunc[9].wfunc        =          1.00
   ScFunc[9].distr_type   =       F_GAUSS

Function 10 = Charged_AA_Penalty_Spacer : penalty for charged AA (DEKRH) in spacer (H=2/3)
   Parameters:
   ScFunc[10].from         =             3
   ScFunc[10].to           =            11
   ScFunc[10].par1         =         -4.00 penalty
   ScFunc[10].par4         =             3 threshold: max number of charged AA in spacer
   ScFunc[10].wfunc        =          1.00

Function 11 = Flexibility_Spacer : contents of PVI in spacer
   Parameters:
   ScFunc[11].from         =             3
   ScFunc[11].to           =             8
   ScFunc[11].par1         =         -4.00 penalty
   ScFunc[11].par4         =             4 par4 non-flexible residues are max allowed
   ScFunc[11].wfunc        =          1.00

Function 12 = PenaltyForBadProfile : penalty for bad profile in hydrophobic tail
   Parameters:
   ScFunc[12].from         =            10
   ScFunc[12].to           =   PROFILE_END
   ScFunc[12].par1         =          0.20 threshold
   ScFunc[12].par2         =        -12.00 penalty
   ScFunc[12].wfunc        =          1.00

 Function 13 = Higher_Average: function for hydrophobic region [10..C_end] (for at least the par4=8 last AAs)
   Parameters:
   ScFunc[13].from         =            10
   ScFunc[13].to           = SEQUENCE_CEND
   ScFunc[13].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[13].par1         =         12.35 mean hydrophobicity for at least the 8 last AAs was calculated
   ScFunc[13].par2         =          1.57 dispersion was calculated
   ScFunc[13].par4         =             8 minimal length of hydrophobic region
   ScFunc[13].wfunc        =          1.00
   ScFunc[13].distr_type   =       F_GAUSS

Function 14 = Higher_Average : function for hydrophobic tail [26..C_end](for at least the par4=8 last AAs)
   Parameters:
   ScFunc[14].from         =            26 (after profile-end)
   ScFunc[14].to           = SEQUENCE_CEND
   ScFunc[14].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[14].par1         =         12.44 mean hydrophobicity for at least the 8 last AAs was calculated
   ScFunc[14].par2         =          2.49 dispersion was calculated
   ScFunc[14].par4         =             8 minimal length of tail for calculation of hydrophobicity parameters
   ScFunc[14].wfunc        =          1.00
   ScFunc[14].distr_type   =       F_GAUSS

Function 15 = Sliding_Window : penalty for too short even hydrophobic section
   Parameters:
   ScFunc[15].from         =             9
   ScFunc[15].to           = SEQUENCE_CEND
   ScFunc[15].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[15].par1         =          9.00 threshold for windows containig Leu (min mean window hydrophobicity)
   ScFunc[15].par2         =          6.00 threshold for windows without Leu
   ScFunc[15].par3         =        -12.00 penalty
   ScFunc[15].par4         =             4 winlen
   ScFunc[15].par5         =             5 min number of windows one after another
   ScFunc[15].wfunc        =          1.00

Function 16 = Post_Sliding_Window_Polar_Penalty : penalty for polar windows in the hydrophobic tail
   Parameters:
   ScFunc[16].from         =            10
   ScFunc[16].to           = SEQUENCE_CEND
   ScFunc[16].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[16].par1         =          1.50 minimum of mean hydrophobicity per window
   ScFunc[16].par2         =         -4.00 penalty
   ScFunc[16].par3         =          0.50 threshold for extreme windows
   ScFunc[16].par4         =             3 winlen
   ScFunc[16].wfunc        =          1.00

Function 17 = Post_Sliding_Window_SGC_Penalty : penalty for too long SGC - sections (len = par4) in hydrophobic tail
   Parameters:
   ScFunc[17].from         =             9
   ScFunc[17].to           = SEQUENCE_CEND
   ScFunc[17].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[17].par1         =        -12.00 penalty
   ScFunc[17].par2         =          8.20 threshold for hydrophobicity of a window with len=(winlen+1)
   ScFunc[17].par4         =             3 winlen
   ScFunc[17].par5         =             2 are max allowed per window 
   ScFunc[17].wfunc        =          1.00

Function 18 = LVI_contents : contents of Leu, Val, Ile in the hydrophobic tail
   Parameters:
   ScFunc[18].from         =            10
   ScFunc[18].to           = SEQUENCE_CEND
   ScFunc[18].par1         =         15.00 threshold
   ScFunc[18].par2         =        -12.00 penalty
   ScFunc[18].wfunc        =          1.00

Function 19 = Combi_FWHY_contents_2win : penalty if more than 40% WHFY and 2 disconnected windows (l=4) with > 2 aromats
   Parameters:
   ScFunc[19].from         =             9
   ScFunc[19].to           = SEQUENCE_CEND
   ScFunc[19].PropertyName =    ZVEL_AROMA WHFY sections
   ScFunc[19].par1         =         40.00 threshold: percentage of aromats in tail
   ScFunc[19].par2         =        -12.00 penalty
   ScFunc[19].par4         =             4 winlen
   ScFunc[19].par5         =             2 aromats are max allowed per window if par1 is exceeded
   ScFunc[19].wfunc        =          1.00

Function 20 = Sliding_Window : penalty for small (according to volume) windows in tail 
   Parameters:
   ScFunc[20].from         =             9
   ScFunc[20].to           = SEQUENCE_CEND
   ScFunc[20].PropertyName =    HAGECH94_V volume scale
   ScFunc[20].par1         =        110.00 threshold (min mean window volume)
   ScFunc[20].par2         =        -12.00 penalty
   ScFunc[20].par4         =             4 winlen
   ScFunc[20].par5         =             5 min number of windows one after another
   ScFunc[20].wfunc        =          1.00

Function 21 = Sum2 : volume function for two positions
   Parameters:
   ScFunc[21].from         =            -1 Position 1
   ScFunc[21].to           =             2 Position 2
   ScFunc[21].PropertyName =    HAGECH94_V mean volume of residues
   ScFunc[21].par1         =        203.85 mean volume was calculated
   ScFunc[21].par2         =         33.01 dispersion was calculated
   ScFunc[21].wfunc        =          0.50
   ScFunc[21].distr_type   =       F_GAUSS



Last modified: 28th October 2002