
                                  hmoment 



Function

   Calculate and plot hydrophobic moment for protein sequence(s)

Description

   hmoment plots or writes out the hydrophobic moment calculated for
   overlapping windows over one or more input protein sequences. The
   hydrophic moment reflects the periodicity of hydrophobicity of a
   peptide, as measured per residue for a specified angle of rotation.
   The window size, alpha helix angle, and beta sheet angle are
   user-specified. The alpha helix moment and beta sheet moment may be
   plotted or output.

Algorithm

   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.

Usage

   Here is a sample session with hmoment


% hmoment tsw:hbb_human 
Calculate and plot hydrophobic moment for protein sequence(s)
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, gif)
*  -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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               Reviewed;         147 AA.
AC   P68871; P02023; Q13852; Q14481; Q14510; Q45KT0; Q6FI08; Q8IZI1;
AC   Q9BX96; Q9UCP8; Q9UCP9;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 2.
DT   20-MAR-2007, entry version 43.
DE   Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin).
GN   Name=HBB;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE.
RX   MEDLINE=81064667; PubMed=6254664; DOI=10.1016/0092-8674(80)90428-6;
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   [2]
RP   NUCLEOTIDE SEQUENCE.
RX   MEDLINE=77126403; PubMed=1019344;
RA   Marotta C., Forget B., Cohen-Solal M., Weissman S.M.;
RT   "Nucleotide sequence analysis of coding and noncoding regions of human
RT   beta-globin mRNA.";
RL   Prog. Nucleic Acid Res. Mol. Biol. 19:165-175(1976).
RN   [3]
RP   NUCLEOTIDE SEQUENCE.
RA   Lu L., Hu Z.H., Du C.S., Fu Y.S.;
RT   "DNA sequence of the human beta-globin gene isolated from a healthy
RT   Chinese.";
RL   Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE, AND VARIANT DURHAM-N.C. PRO-115.
RC   TISSUE=Blood;
RA   Kutlar F., Abboud M., Leithner C., Holley L., Brisco J., Kutlar A.;
RT   "Electrophoretically silent, very unstable, thalassemic mutation at
RT   codon 114 of beta globin (hemoglobin Durham-N.C.) detected by cDNA
RT   sequencing of mRNA, from a Russian women.";
RL   Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   NUCLEOTIDE SEQUENCE, AND VARIANT LOUISVILLE LEU-43.
RC   TISSUE=Blood;
RA   Kutlar F., Harbin J., Brisco J., Kutlar A.;
RT   "Rapid detection of electrophoretically silent, unstable human
RT   hemoglobin 'Louisville', (Beta; Phe 42 Leu/TTT to CTT) by cDNA
RT   sequencing of mRNA.";
RL   Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   NUCLEOTIDE SEQUENCE, AND VARIANT TY GARD GLN-125.


  [Part of this file has been deleted for brevity]

FT   VARIANT     141    141       A -> T (in St Jacques: O(2) affinity up).
FT                                /FTId=VAR_003081.
FT   VARIANT     141    141       A -> V (in Puttelange; polycythemia; O(2)
FT                                affinity up).
FT                                /FTId=VAR_003082.
FT   VARIANT     142    142       L -> R (in Olmsted; unstable).
FT                                /FTId=VAR_003083.
FT   VARIANT     143    143       A -> D (in Ohio; O(2) affinity up).
FT                                /FTId=VAR_003084.
FT   VARIANT     144    144       H -> D (in Rancho Mirage).
FT                                /FTId=VAR_003085.
FT   VARIANT     144    144       H -> P (in Syracuse; O(2) affinity up).
FT                                /FTId=VAR_003087.
FT   VARIANT     144    144       H -> Q (in Little Rock; O(2) affinity
FT                                up).
FT                                /FTId=VAR_003086.
FT   VARIANT     144    144       H -> R (in Abruzzo; O(2) affinity up).
FT                                /FTId=VAR_003088.
FT   VARIANT     145    145       K -> E (in Mito; O(2) affinity up).
FT                                /FTId=VAR_003089.
FT   VARIANT     146    146       Y -> C (in Rainier; O(2) affinity up).
FT                                /FTId=VAR_003090.
FT   VARIANT     146    146       Y -> H (in Bethesda; O(2) affinity up).
FT                                /FTId=VAR_003091.
FT   VARIANT     147    147       H -> D (in Hiroshima; O(2) affinity up).
FT                                /FTId=VAR_003092.
FT   VARIANT     147    147       H -> L (in Cowtown; O(2) affinity up).
FT                                /FTId=VAR_003093.
FT   VARIANT     147    147       H -> P (in York; O(2) affinity up).
FT                                /FTId=VAR_003094.
FT   VARIANT     147    147       H -> Q (in Kodaira; O(2) affinity up).
FT                                /FTId=VAR_003095.
FT   HELIX         5     15
FT   TURN         20     22
FT   HELIX        23     34
FT   HELIX        36     41
FT   HELIX        43     45
FT   HELIX        51     56
FT   HELIX        58     76
FT   TURN         77     79
FT   HELIX        81     93
FT   TURN         94     96
FT   HELIX       101    118
FT   HELIX       119    121
FT   HELIX       124    141
FT   HELIX       143    145
SQ   SEQUENCE   147 AA;  15998 MW;  A31F6D621C6556A1 CRC64;
     MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
     VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
     KEFTPPVQAA YQKVVAGVAN ALAHKYH
//

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 147

Window: 10 Angle: 100 Max uH: 0.714
Position        uH
1               0.086
2               0.091
3               0.216
4               0.208
5               0.123
6               0.211
7               0.194
8               0.185
9               0.169
10              0.312
11              0.292
12              0.185
13              0.092
14              0.050
15              0.164
16              0.245
17              0.187
18              0.130
19              0.262
20              0.396
21              0.317
22              0.342
23              0.492
24              0.508
25              0.517
26              0.418
27              0.416
28              0.350
29              0.292
30              0.196
31              0.102
32              0.288
33              0.314
34              0.442
35              0.560
36              0.464
37              0.577
38              0.584
39              0.676
40              0.714
41              0.670
42              0.462
43              0.369
44              0.221
45              0.176
46              0.073


  [Part of this file has been deleted for brevity]

88              0.179
89              0.201
90              0.065
91              0.041
92              0.110
93              0.181
94              0.261
95              0.312
96              0.200
97              0.263
98              0.369
99              0.310
100             0.362
101             0.495
102             0.585
103             0.450
104             0.488
105             0.547
106             0.315
107             0.311
108             0.252
109             0.187
110             0.215
111             0.295
112             0.425
113             0.303
114             0.421
115             0.528
116             0.487
117             0.436
118             0.501
119             0.532
120             0.409
121             0.447
122             0.308
123             0.383
124             0.252
125             0.361
126             0.374
127             0.314
128             0.219
129             0.310
130             0.361
131             0.439
132             0.433
133             0.507
134             0.336
135             0.344
136             0.207
137             0.234
138             0.299

Data files

   None.

Notes

   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.

   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.

   The -plot option must be specified to produce a plot. 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.

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 using GOR method
   helixturnhelix Identify nucleic acid-binding motifs in protein
   sequences
   pepcoil Predicts coiled coil regions in protein sequences
   pepnet Draw a helical net for a protein sequence
   pepwheel Draw a helical wheel diagram for a protein sequence
   tmap Predict and plot transmembrane segments in protein sequences

Author(s)

   Alan Bleasby (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, 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

   None
