| hmoment

## Wiki

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Please help by correcting and extending the Wiki pages.

## 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:6.6.0.0

       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
       -squick1            boolean    Read id and sequence only
       -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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-seqall] (Parameter 1) | seqall | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
-graph | xygraph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg | EMBOSS_GRAPHICS value, or x11
-outfile | outfile | Output file name | Output file | <*>.hmoment
Additional (Optional) qualifiers
-window | integer | Window | Any integer value | 10
-aangle | integer | Alpha helix angle (degrees) | Any integer value | 100
-bangle | integer | Beta sheet angle (degrees) | Any integer value | 160
Advanced (Unprompted) qualifiers
-baseline | float | Graph marker line | Any numeric value | 0.35
-plot | toggle | Produce graphic | Toggle value Yes/No | No
-double | boolean | Plot two graphs | Boolean value Yes/No | No
Associated qualifiers
"-seqall" associated seqall qualifiers
-sbegin1 -sbegin_seqall | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_seqall | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_seqall | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_seqall | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_seqall | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_seqall | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_seqall | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_seqall | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_seqall | boolean | Sequence is circular | Boolean value Yes/No | N
-squick1 -squick_seqall | boolean | Read id and sequence only | Boolean value Yes/No | N
-sformat1 -sformat_seqall | string | Input sequence format | Any string |
-iquery1 -iquery_seqall | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_seqall | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_seqall | string | Database name | Any string |
-sid1 -sid_seqall | string | Entryname | Any string |
-ufo1 -ufo_seqall | string | UFO features | Any string |
-fformat1 -fformat_seqall | string | Features format | Any string |
-fopenfile1 -fopenfile_seqall | string | Features file name | Any string |
"-graph" associated xygraph qualifiers
-gprompt | boolean | Graph prompting | Boolean value Yes/No | N
-gdesc | string | Graph description | Any string |
-gtitle | string | Graph title | Any string |
-gsubtitle | string | Graph subtitle | Any string |
-gxtitle | string | Graph x axis title | Any string |
-gytitle | string | Graph y axis title | Any string |
-goutfile | string | Output file for non interactive displays | Any string |
-gdirectory | string | Output directory | Any string |
"-outfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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 © 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