                                   hmoment



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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

Calculate and plot hydrophobic moment for protein sequence(s)
Version: EMBOSS:6.5.6.0

   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,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)
*  -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
   -scircular1         boolean    Sequence is circular
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   hmoment reads one or protein sequences.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  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; A4GX73; B2ZUE0; P02023; Q13852; Q14481; Q14510; Q45KT0;
AC   Q549N7; Q6FI08; Q6R7N2; Q8IZI1; Q9BX96; Q9UCD6; Q9UCP8; Q9UCP9;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 2.
DT   13-JUN-2012, entry version 108.
DE   RecName: Full=Hemoglobin subunit beta;
DE   AltName: Full=Beta-globin;
DE   AltName: Full=Hemoglobin beta chain;
DE   Contains:
DE     RecName: Full=LVV-hemorphin-7;
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 [GENOMIC DNA].
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   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
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   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT LYS-7.
RX   PubMed=16175509; DOI=10.1086/491748;
RA   Wood E.T., Stover D.A., Slatkin M., Nachman M.W., Hammer M.F.;
RT   "The beta-globin recombinational hotspot reduces the effects of strong
RT   selection around HbC, a recently arisen mutation providing resistance
RT   to malaria.";
RL   Am. J. Hum. Genet. 77:637-642(2005).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
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   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT ARG-113.
RA   Cabeda J.M., Correia C., Estevinho A., Cardoso C., Amorim M.L.,
RA   Cleto E., Vale L., Coimbra E., Pinho L., Justica B.;
RT   "Unexpected patterns of globin mutations in thalassemia patients from
RT   north of Portugal.";


  [Part of this file has been deleted for brevity]

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   CONFLICT     26     26       Missing (in Ref. 15; ACD39349).
FT   CONFLICT     42     42       F -> L (in Ref. 13; AAR96398).
FT   HELIX         6     16
FT   TURN         21     23
FT   HELIX        24     35
FT   HELIX        37     42
FT   HELIX        44     46
FT   HELIX        52     57
FT   HELIX        59     77
FT   TURN         78     80
FT   HELIX        82     94
FT   TURN         95     97
FT   HELIX       102    119
FT   HELIX       120    122
FT   HELIX       125    142
FT   HELIX       144    146
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.

   The output is to the specified graphics device.

   The results can be output in one of several formats by using the
   command-line qualifier -graph xxx, where 'xxx' is replaced by the name
   of the required device. Support depends on the availability of
   third-party software packages.

   The device names that output to a file are: ps (postscript), cps
   (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.

   The other available device names are: meta, x11 (xwindows), tek
   (tek4107t), tekt (tektronix), xterm, text.

   Output can be turned off by specifying none (null).

   See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further
   information on supported devices.

   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
   charge           Draw a protein charge plot
   iep              Calculate the isoelectric point of proteins
   octanol          Draw a White-Wimley protein hydropathy plot
   pepinfo          Plot amino acid properties of a protein sequence in parallel
   pepstats         Calculate statistics of protein properties
   pepwindow        Draw a hydropathy plot for a protein sequence
   pepwindowall     Draw Kyte-Doolittle hydropathy plot for a protein
                    alignment

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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
