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<HTML>
<HEAD>
<TITLE>
EMBOSS: hmoment
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
hmoment
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Hydrophobic moment calculation
<H2>
Description
</H2>
<b>hmoment</b> plots or writes out the hydrophobic moment. Hydrophic
moment is the hydrophobicity of a peptide measured for a specified angle
of rotation per residue.
<p>
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.
<p>
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.
<p>
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.
<p>
<b>hmoment</b> 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.
<H2>
Usage
</H2>
<b>Here is a sample session with hmoment</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>hmoment tsw:hbb_human </b>
Hydrophobic moment calculation
Output file [hbb_human.hmoment]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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 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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-seqall]<br>(Parameter 1)</td>
<td>Protein sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-graph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>
<tr>
<td>-outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.hmoment</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-window</td>
<td>Window</td>
<td>Any integer value</td>
<td>10</td>
</tr>
<tr>
<td>-aangle</td>
<td>Alpha helix angle (degrees)</td>
<td>Any integer value</td>
<td>100</td>
</tr>
<tr>
<td>-bangle</td>
<td>Beta sheet angle (degrees)</td>
<td>Any integer value</td>
<td>160</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-baseline</td>
<td>Graph marker line</td>
<td>Any numeric value</td>
<td>0.35</td>
</tr>
<tr>
<td>-plot</td>
<td>Produce graphic</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-double</td>
<td>Plot two graphs</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>hmoment</b> reads in a protein sequence USA.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tsw:hbb_human' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:hbb_human</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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.
<font color=red> [Part of this file has been deleted for brevity]</font>
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
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
With the '-plot' option <b>hmoment</b> 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.
<p>
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.)
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: hbb_human.hmoment</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
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
<font color=red> [Part of this file has been deleted for brevity]</font>
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
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
<ol>
<li>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
</ol>
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="garnier.html">garnier</a></td>
<td>Predicts protein secondary structure</td>
</tr>
<tr>
<td><a href="helixturnhelix.html">helixturnhelix</a></td>
<td>Report nucleic acid binding motifs</td>
</tr>
<tr>
<td><a href="pepcoil.html">pepcoil</a></td>
<td>Predicts coiled coil regions</td>
</tr>
<tr>
<td><a href="pepnet.html">pepnet</a></td>
<td>Displays proteins as a helical net</td>
</tr>
<tr>
<td><a href="pepwheel.html">pepwheel</a></td>
<td>Shows protein sequences as helices</td>
</tr>
<tr>
<td><a href="tmap.html">tmap</a></td>
<td>Displays membrane spanning regions</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Written (March 2001) - Alan Bleasby.
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
</BODY>
</HTML>