File: pepinfo.html

package info (click to toggle)
emboss 5.0.0-7
links: PTS, VCS
area: main
in suites: lenny
size: 81,332 kB
ctags: 25,201
sloc: ansic: 229,873; java: 29,051; sh: 10,636; perl: 8,714; makefile: 1,227; csh: 520; asm: 351; pascal: 237; xml: 94; modula3: 8
file content (693 lines) | stat: -rw-r--r-- 21,269 bytes
<HTML>

<HEAD>
  <TITLE>
  EMBOSS: pepinfo
  </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">
pepinfo
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>

<H2>
    Function
</H2>
Plots simple amino acid properties in parallel

<H2>
    Description
</H2>


pepinfo detects and displays various useful metrics about a protein
sequence. 

<p>
It can plot and display the following properties:

<ul>

<li>plots of hydrophobicity (using the method of Kyte & Doolittle), of
OHM (Sweet & Eisenberg), or of consensus parameters (Eisenberg et al))

<li>a histogram of the presence of residues with the physico-chemical
properties: Tiny, Small, Aliphatic, Aromatic, Non-polar, Polar,
Charged, Positive, Negative.

</ul>

<p>
The data are also written out to a data file.

<H2>
    Usage
</H2>
<b>Here is a sample session with pepinfo</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>pepinfo </b>
Plots simple amino acid properties in parallel
Input protein sequence: <b>tsw:opsd_human</b>
Graph type [x11]: <b>cps</b>
Output file [opsd_human.pepinfo]: <b></b>

Created pepinfo.ps

</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:
  [-sequence]          sequence   Protein sequence 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    [*.pepinfo] Output file name

   Additional (Optional) qualifiers:
   -aaproperties       datafile   [Eaa_properties.dat] Amino acid chemical
                                  classes data file
   -aahydropathy       datafile   [Eaa_hydropathy.dat] Amino acid hydropathy
                                  values data file
   -hwindow            integer    [9] Window size for hydropathy averaging
                                  (Integer 1 or more)

   Advanced (Unprompted) qualifiers:
   -[no]generalplot    boolean    [Y] Plot histogram of general properties
   -[no]hydropathyplot boolean    [Y] Plot graphs of hydropathy

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the 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
   -odirectory2        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>[-sequence]<br>(Parameter 1)</td>
<td>Protein sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</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]<br>(Parameter 2)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.pepinfo</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>-aaproperties</td>
<td>Amino acid chemical classes data file</td>
<td>Data file</td>
<td>Eaa_properties.dat</td>
</tr>

<tr>
<td>-aahydropathy</td>
<td>Amino acid hydropathy values data file</td>
<td>Data file</td>
<td>Eaa_hydropathy.dat</td>
</tr>

<tr>
<td>-hwindow</td>
<td>Window size for hydropathy averaging</td>
<td>Integer 1 or more</td>
<td>9</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>-[no]generalplot</td>
<td>Plot histogram of general properties</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-[no]hydropathyplot</td>
<td>Plot graphs of hydropathy</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

</table>


<H2>
    Input file format
</H2>

<b>pepinfo</b> reads a protein sequence USA.

<p>


<a name="input.1"></a>
<h3>Input files for usage example </h3>

'tsw:opsd_human' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:opsd_human</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   OPSD_HUMAN              Reviewed;         348 AA.
AC   P08100; Q16414; Q2M249;
DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1988, sequence version 1.
DT   20-MAR-2007, entry version 91.
DE   Rhodopsin (Opsin-2).
GN   Name=RHO; Synonyms=OPN2;
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=84272729; PubMed=6589631;
RA   Nathans J., Hogness D.S.;
RT   "Isolation and nucleotide sequence of the gene encoding human
RT   rhodopsin.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
RA   Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
RT   "Genome-wide discovery and analysis of human seven transmembrane helix
RT   receptor genes.";
RL   Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Retina;
RG   The German cDNA consortium;
RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
RX   PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
RA   Bennett J., Beller B., Sun D., Kariko K.;
RT   "Sequence analysis of the 5.34-kb 5' flanking region of the human
RT   rhodopsin-encoding gene.";
RL   Gene 167:317-320(1995).
RN   [6]
RP   REVIEW ON RP4 VARIANTS.
RX   MEDLINE=94004905; PubMed=8401533;
RA   Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
RA   Bhattacharya S.;


<font color=red>  [Part of this file has been deleted for brevity]</font>

FT                                /FTId=VAR_004816.
FT   VARIANT     209    209       V -&gt; M (effect not known).
FT                                /FTId=VAR_004817.
FT   VARIANT     211    211       H -&gt; P (in RP4).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -&gt; R (in RP4).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -&gt; K (in RP4).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -&gt; C (in RP4).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -&gt; R (in RP4).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       Missing (in RP4).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       Missing (in RP4).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -&gt; L (in RP4).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -&gt; R (in RP4).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -&gt; E (in CSNBAD1).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -&gt; E (in RP4).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -&gt; R (in RP4).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -&gt; M (in RP4).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -&gt; L (in RP4).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -&gt; M (in RP4).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -&gt; A (in RP4).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -&gt; L (in RP4; common variant).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -&gt; Q (in RP4).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -&gt; R (in RP4).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -&gt; S (in RP4).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;
     MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
     VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
     GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
     EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
     ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
     YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//
</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>

Graphs are written to the selected graphics device.

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: opsd_human.pepinfo </h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Printing out Tiny residues in OPSD_HUMAN from position 1 to 348

Position  Residue			Result
       1       M                               0
       2       N                               0
       3       G                               1
       4       T                               1
       5       E                               0
       6       G                               1
       7       P                               0
       8       N                               0
       9       F                               0
      10       Y                               0
      11       V                               0
      12       P                               0
      13       F                               0
      14       S                               1
      15       N                               0
      16       A                               1
      17       T                               1
      18       G                               1
      19       V                               0
      20       V                               0
      21       R                               0
      22       S                               1
      23       P                               0
      24       F                               0
      25       E                               0
      26       Y                               0
      27       P                               0
      28       Q                               0
      29       Y                               0
      30       Y                               0
      31       L                               0
      32       A                               1
      33       E                               0
      34       P                               0
      35       W                               0
      36       Q                               0
      37       F                               0
      38       S                               1
      39       M                               0
      40       L                               0
      41       A                               1
      42       A                               1
      43       Y                               0
      44       M                               0
      45       F                               0
      46       L                               0
      47       L                               0


<font color=red>  [Part of this file has been deleted for brevity]</font>

  301       Y                           0.500
  302       N                           0.549
  303       P                           0.633
  304       V                           0.636
  305       I                           0.553
  306       Y                           0.438
  307       I                           0.358
  308       M                           0.250
  309       M                           0.262
  310       N                          -0.172
  311       K                          -0.288
  312       Q                          -0.409
  313       F                          -0.409
  314       R                          -0.362
  315       N                          -0.281
  316       C                          -0.120
  317       M                           0.128
  318       L                           0.028
  319       T                           0.341
  320       T                           0.481
  321       I                           0.282
  322       C                           0.124
  323       C                           0.020
  324       G                           0.143
  325       K                           0.202
  326       N                          -0.051
  327       P                          -0.183
  328       L                          -0.298
  329       G                          -0.282
  330       D                          -0.136
  331       D                           0.020
  332       E                           0.001
  333       A                           0.003
  334       S                          -0.070
  335       A                          -0.137
  336       T                          -0.042
  337       V                          -0.042
  338       S                          -0.117
  339       K                          -0.117
  340       T                          -0.280
  341       E                          -0.154
  342       T                          -0.206
  343       S                          -0.172
  344       Q                           0.063
  345       V                           0.000
  346       A                           0.000
  347       P                           0.000
  348       A                           0.000



</pre>
</td></tr></table><p>
<p><h3>Graphics File: pepinfo.ps</h3>
<p><img src="pepinfo.1.pepinfo.gif" alt="[pepinfo results]">

<p>

The output file 'pepinfo.out' contains the coordinates from the graphs.

<p>

For the first set of graphs, 9 sets of true/false values are written out.
For the second set of graphs, 3 sets of hydrophobicity values are written.

<H2>
    Data files
</H2>


The physico-chemical properties of the residues are read from the EMBOSS
data file 'Eaa_properties.dat'.  This file can be copied into your
current directory and inspected ot altered by using the application
'embossdata -fetch'.  Another file can be specified using the qualifier
'-aaproperties'.

<p>
The hydropathy data of the residues are read from the EMBOSS data file
'Eaa_hydropathy.dat'.  This file can be copied into your current
directory and inspected ot altered by using the application 'embossdata
-fetch'.  Another file can be specified using the qualifier
'-aahydropathy'. 

<p>
EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by EMBOSS environment variable EMBOSS_DATA.

<p>

Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".

<p>
The directories are searched in the following order:

<ul>
   <li> . (your current directory)
   <li> .embossdata (under your current directory)
   <li> ~/ (your home directory)
   <li> ~/.embossdata
</ul>

<H2>
    Notes
</H2>

None.

<H2>
    References
</H2>


<ol>

<li>
Kyte J, Doolittle RF 
A simple method for displaying the hydropathic character of a protein. 
J Mol Biol 1982 May 5;157(1):105-132

<li>
Sweet RM, Eisenberg D 
Correlation of sequence hydrophobicities measures similarity in
three-dimensional protein structure. 
J Mol Biol 1983 Dec 25;171(4):479-488

<li>
Eisenberg D, Weiss RM, Terwilliger TC.
The helical hydrophobic moment: a measure of the amphiphilicity of a
helix. 
Nature 1982 Sep 23;299(5881):371-4

</ol>

<H2>
    Warnings
</H2>


None.

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>

It always exits with a status of 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="backtranambig.html">backtranambig</a></td>
<td>Back translate a protein sequence to ambiguous codons</td>
</tr>

<tr>
<td><a href="backtranseq.html">backtranseq</a></td>
<td>Back translate a protein sequence</td>
</tr>

<tr>
<td><a href="charge.html">charge</a></td>
<td>Protein charge plot</td>
</tr>

<tr>
<td><a href="checktrans.html">checktrans</a></td>
<td>Reports STOP codons and ORF statistics of a protein</td>
</tr>

<tr>
<td><a href="compseq.html">compseq</a></td>
<td>Count composition of dimer/trimer/etc words in a sequence</td>
</tr>

<tr>
<td><a href="emowse.html">emowse</a></td>
<td>Protein identification by mass spectrometry</td>
</tr>

<tr>
<td><a href="freak.html">freak</a></td>
<td>Residue/base frequency table or plot</td>
</tr>

<tr>
<td><a href="iep.html">iep</a></td>
<td>Calculates the isoelectric point of a protein</td>
</tr>

<tr>
<td><a href="mwcontam.html">mwcontam</a></td>
<td>Shows molwts that match across a set of files</td>
</tr>

<tr>
<td><a href="mwfilter.html">mwfilter</a></td>
<td>Filter noisy molwts from mass spec output</td>
</tr>

<tr>
<td><a href="octanol.html">octanol</a></td>
<td>Displays protein hydropathy</td>
</tr>

<tr>
<td><a href="pepstats.html">pepstats</a></td>
<td>Protein statistics</td>
</tr>

<tr>
<td><a href="pepwindow.html">pepwindow</a></td>
<td>Displays protein hydropathy</td>
</tr>

<tr>
<td><a href="pepwindowall.html">pepwindowall</a></td>
<td>Displays protein hydropathy of a set of sequences</td>
</tr>

</table>


<H2>
    Author(s)
</H2>


Mark Faller (current e-mail address unknown)
<br>
while he was with:
<br>
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK


<H2>
    History
</H2>

Written (1999) - Mark Faller

<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>