hmoment.txt

emboss的linux版本的源代码

                                  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 tsw:hbb_human 
Hydrophobic moment calculation
Output file [hbb_human.hmoment]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-seqall]            seqall     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, xterm, png)
*  -outfile            outfile    [*.hmoment] Output file name

   Additional (Optional) qualifiers:
   -window             integer    [10] Window (Any integer value)
   -aangle             integer    [100] Alpha helix angle (degrees) (Any
                                  integer value)
   -bangle             integer    [160] Beta sheet angle (degrees) (Any
                                  integer value)

   Advanced (Unprompted) qualifiers:
   -baseline           float      [0.35] Graph marker line (Any numeric value)
   -plot               toggle     [N] Produce graphic
   -double             boolean    [N] Plot two graphs

   Associated qualifiers:

   "-seqall" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   hmoment reads in a protein sequence USA.

  Input files for usage example

   'tsw:hbb_human' is a sequence entry in the example protein database
   'tsw'

  Database entry: tsw:hbb_human

ID   HBB_HUMAN      STANDARD;      PRT;   146 AA.
AC   P02023;
DT   21-JUL-1986 (Rel. 01, Created)
DT   21-JUL-1986 (Rel. 01, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   HEMOGLOBIN BETA CHAIN.
GN   HBB.
OS   Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS   Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN   [1]
RP   SEQUENCE.
RC   SPECIES=HUMAN;
RA   BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA   RUDLOFF V., WITTMANN-LIEBOLD B.;
RT   "The constitution of normal adult human haemoglobin.";
RL   Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   SPECIES=HUMAN;
RX   MEDLINE; 81064667.
RA   LAWN R.M., EFSTRATIADIS A., O'CONNELL C., MANIATIS T.;
RT   "The nucleotide sequence of the human beta-globin gene.";
RL   Cell 21:647-651(1980).
RN   [3]
RP   SEQUENCE OF 121-146 FROM N.A.
RC   SPECIES=HUMAN;
RX   MEDLINE; 85205333.
RA   LANG K.M., SPRITZ R.A.;
RT   "Cloning specific complete polyadenylylated 3'-terminal cDNA
RT   segments.";
RL   Gene 33:191-196(1985).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF DEOXYHEMOGLOBIN.
RC   SPECIES=HUMAN;
RX   MEDLINE; 76027820.
RA   FERMI G.;
RT   "Three-dimensional fourier synthesis of human deoxyhaemoglobin at
RT   2.5-A resolution: refinement of the atomic model.";
RL   J. Mol. Biol. 97:237-256(1975).
RN   [5]
RP   SEQUENCE.
RC   SPECIES=P.TROGLODYTES;
RX   MEDLINE; 66071496.
RA   RIFKIN D.B., KONIGSBERG W.;
RT   "The characterization of the tryptic peptides from the hemoglobin of
RT   the chimpanzee (Pan troglodytes).";
RL   Biochim. Biophys. Acta 104:457-461(1965).
RN   [6]


  [Part of this file has been deleted for brevity]

FT   VARIANT     140    140       A -> T (IN ST JACQUES: O2 AFFINITY UP).
FT                                /FTId=VAR_003081.
FT   VARIANT     140    140       A -> V (IN PUTTELANGE; POLYCYTHEMIA;
FT                                O2 AFFINITY UP).
FT                                /FTId=VAR_003082.
FT   VARIANT     141    141       L -> R (IN OLMSTED; UNSTABLE).
FT                                /FTId=VAR_003083.
FT   VARIANT     142    142       A -> D (IN OHIO; O2 AFFINITY UP).
FT                                /FTId=VAR_003084.
FT   VARIANT     143    143       H -> D (IN RANCHO MIRAGE).
FT                                /FTId=VAR_003085.
FT   VARIANT     143    143       H -> Q (IN LITTLE ROCK; O2 AFFINITY UP).
FT                                /FTId=VAR_003086.
FT   VARIANT     143    143       H -> P (IN SYRACUSE; O2 AFFINITY UP).
FT                                /FTId=VAR_003087.
FT   VARIANT     143    143       H -> R (IN ABRUZZO; O2 AFFINITY UP).
FT                                /FTId=VAR_003088.
FT   VARIANT     144    144       K -> E (IN MITO; O2 AFFINITY UP).
FT                                /FTId=VAR_003089.
FT   VARIANT     145    145       Y -> C (IN RAINIER; O2 AFFINITY UP).
FT                                /FTId=VAR_003090.
FT   VARIANT     145    145       Y -> H (IN BETHESDA; O2 AFFINITY UP).
FT                                /FTId=VAR_003091.
FT   VARIANT     146    146       H -> D (IN HIROSHIMA; O2 AFFINITY UP).
FT                                /FTId=VAR_003092.
FT   VARIANT     146    146       H -> L (IN COWTOWN; O2 AFFINITY UP).
FT                                /FTId=VAR_003093.
FT   VARIANT     146    146       H -> P (IN YORK; O2 AFFINITY UP).
FT                                /FTId=VAR_003094.
FT   VARIANT     146    146       H -> Q (IN KODAIRA; O2 AFFINITY UP).
FT                                /FTId=VAR_003095.
FT   HELIX         5     15
FT   TURN         16     17
FT   HELIX        20     34
FT   HELIX        36     41
FT   HELIX        43     45
FT   HELIX        51     55
FT   TURN         56     56
FT   HELIX        58     75
FT   TURN         76     77
FT   HELIX        78     94
FT   TURN         95     96
FT   TURN        100    100
FT   HELIX       101    121
FT   HELIX       124    142
FT   TURN        143    144
SQ   SEQUENCE   146 AA;  15867 MW;  EC9744C9 CRC32;
     VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
     KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
     EFTPPVQAAY QKVVAGVANA LAHKYH
//

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.)

  Output files for usage example

  File: hbb_human.hmoment

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


  [Part of this file has been deleted for brevity]

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

    1. 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)

   Alan Bleasby (ajb