
                              EMBOSS: hmoment
     _________________________________________________________________
   
                                Program hmoment
                                       
Function

   Hydrophobic moment calculation
   
Description

   hmoment plots or writes out the hydrophobic moment. Hydrophic moment
   is the hydrophobicity of a peptide measured for a specified angle of
   rotation per residue.
   
   Periodicities in the polar/apolar character of the amino acid sequence
   of a protein can be examined by assigning to each residue a numerical
   hydrophobicity and searching for periodicity in the resulting
   one-dimensional function. The strength of each periodic component is
   the quantity that has been termed the hydrophobic moment.
   
   When proteins of known three-dimensional structure are examined, it is
   found that sequences that form alpha helices tend to have, on average,
   a strong periodicity in the hydrophobicity of af 3.6 residues, the
   period of the alpha helix. The angle of rotation per residue in alpha
   helices is 100 degrees. Similarly, many sequences that form strands of
   beta sheets tend to have a periodicity in their hydrophobicity of
   about 2.3 residues, the period typical of beta structure. The angle of
   rotation per residue in beta sheets is 160 degrees. This means that
   many protein sequences tend to form the periodic structure that
   maximizes their amphiphilicity.
   
   The hydrophobic moment is measured within a moving window using the
   method of Eisenberg et al. The default angle of 100 degrees is used
   for the alpha-helix results and the default of 160 degrees is used for
   the beta-sheet results. These angles can be changed if required using
   the appropriate options.
   
   hmoment can plot two graphs when the option '-double' is given, one
   for the alpha helix moment and one for the beta sheet moment.
   Otherwise it just plots the alpha helix moment.
   
Usage

   Here is a sample session with hmoment:
   
% hmoment sw:hbb_human
Hydrophobic moment calculation
Output file [hbb_human.hmoment]:

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-seqall]            seqall     Sequence database USA
*  -graph              xygraph    Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers:
   -window             integer    Window
   -bangle             integer    Beta sheet angle (degrees)

   Advanced qualifiers:
   -aangle             integer    Alpha helix angle (degrees)
   -baseline           float      Graph marker line
   -plot               bool       Produce graphic
   -double             bool       Plot two graphs

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-seqall]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -graph Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png EMBOSS_GRAPHICS value, or x11
   -outfile Output file name Output file <sequence>.hmoment
   Optional qualifiers Allowed values Default
   -window Window Any integer value 10
   -bangle Beta sheet angle (degrees) Any integer value 160
   Advanced qualifiers Allowed values Default
   -aangle Alpha helix angle (degrees) Any integer value 100
   -baseline Graph marker line Any integer value 0.35
   -plot Produce graphic Yes/No No
   -double Plot two graphs Yes/No No
   
Input file format

   hmoment reads in a protein sequence.
   
Output file format

   With the '-plot' option hmoment displays a graphical plot of the
   hydrophobic moment of the specified alpha helix angle. With the '-plot
   -double' options it also displays the beta-sheet hydrophobic moment.
   
   Otherwise it writes out a files containing the two columns separated
   by space or TAB characters. The first column is the position of the
   start of the window that the hydrophobic moment was calculated in. The
   second is the hydrophobic moment ('uH'). (If the option '-double' is
   given then the beta-sheet angle hydrophobicity is given as a third
   column.)
   
   The ouput of the above is example follows:
     _________________________________________________________________
   
HMOMENT of HBB_HUMAN from 1 to 146

Window: 10 Angle: 100 Max uH: 0.714
Position        uH
1               0.091
2               0.216
3               0.208
4               0.123
5               0.211
6               0.194
7               0.185
8               0.169
9               0.312
10              0.292
11              0.185
12              0.092
13              0.050
14              0.164
15              0.245
16              0.187
17              0.130
18              0.262
19              0.396
20              0.317
21              0.342
22              0.492
23              0.508
24              0.517
25              0.418
26              0.416
27              0.350
28              0.292
29              0.196
30              0.102
31              0.288
32              0.314
33              0.442
34              0.560
35              0.464
36              0.577
37              0.584
38              0.676
39              0.714
40              0.670
41              0.462
42              0.369
43              0.221
44              0.176
45              0.073
46              0.058
47              0.041
48              0.148
49              0.125
50              0.219
51              0.221
52              0.110
53              0.060
54              0.045
55              0.107
56              0.264
57              0.259
58              0.401
59              0.452
60              0.354
61              0.265
62              0.365
63              0.430
64              0.522
65              0.508
66              0.519
67              0.349
68              0.324
69              0.330
70              0.365
71              0.447
72              0.364
73              0.251
74              0.166
75              0.118
76              0.252
77              0.276
78              0.299
79              0.330
80              0.241
81              0.315
82              0.291
83              0.163
84              0.182
85              0.254
86              0.069
87              0.179
88              0.201
89              0.065
90              0.041
91              0.110
92              0.181
93              0.261
94              0.312
95              0.200
96              0.263
97              0.369
98              0.310
99              0.362
100             0.495
101             0.585
102             0.450
103             0.488
104             0.547
105             0.315
106             0.311
107             0.252
108             0.187
109             0.215
110             0.295
111             0.425
112             0.303
113             0.421
114             0.528
115             0.487
116             0.436
117             0.501
118             0.532
119             0.409
120             0.447
121             0.308
122             0.383
123             0.252
124             0.361
125             0.374
126             0.314
127             0.219
128             0.310
129             0.361
130             0.439
131             0.433
132             0.507
133             0.336
134             0.344
135             0.207
136             0.234
137             0.299
     _________________________________________________________________
   
Data files

   None.
   
Notes

   None.
   
References

   Eisenberg D, Weiss RM, Terwilliger TC "The hydrophobic moment detects
   periodicity in protein hydrophobicity." Proc Natl Acad Sci U S A 1984
   Jan;81(1):140-4
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

    Program name              Description
   garnier        Predicts protein secondary structure
   helixturnhelix Report nucleic acid binding motifs
   pepcoil        Predicts coiled coil regions
   pepnet         Displays proteins as a helical net
   pepwheel       Shows protein sequences as helices
   tmap           Displays membrane spanning regions
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

   Written (March 2001) - Alan Bleasby.
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
