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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: inforesidue
  </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="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
inforesidue
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Return information on a given amino acid residue
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>
    Description
</H2>

<b>inforesidue</b> reports the defined properties for all known residues, or
for any residues specified by the user.





<H2>
    Usage
</H2>

<!--  
	Example usage, as run from the command-line.
        Many examples illustrating different behaviours is good.
 -->

Here is a sample session with <b>inforesidue</b>
<p>

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

% <b>inforesidue </b>
Return information on a given amino acid residue
Amino acid residue code [ABCDEFGHIJKLMNOPQRSTUVWXYZ]: <b></b>
Output file [outfile.inforesidue]: <b></b>

</pre></td></tr></table><p>
<p>
<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>
Return information on a given amino acid residue
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-code]              string     [ABCDEFGHIJKLMNOPQRSTUVWXYZ] Enter IUPAC
                                  amino acids codes, e.g. A, C, D, E etc. (Any
                                  string)
  [-outfile]           outfile    [*.inforesidue] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -aadata             datafile   [Eamino.dat] Amino acid properties
   -mwdata             datafile   [Emolwt.dat] Molecular weight data for amino
                                  acids

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        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

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-code]<br>(Parameter 1)</td>
<td>string</td>
<td>Enter IUPAC amino acids codes, e.g. A, C, D, E etc.</td>
<td>Any string</td>
<td>ABCDEFGHIJKLMNOPQRSTUVWXYZ</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.inforesidue</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-aadata</td>
<td>datafile</td>
<td>Amino acid properties</td>
<td>Data file</td>
<td>Eamino.dat</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-mwdata</td>
<td>datafile</td>
<td>Molecular weight data for amino acids</td>
<td>Data file</td>
<td>Emolwt.dat</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->








<H2>
    Input file format
</H2>

<!-- 
        This includes example input file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null input, etc. 
   -->

<b>inforesidue</b> uses a string of residue codes.

<p>






<H2>
    Output file format
</H2>


<b>inforesidue</b> 
outputs a text table of residue properties.


<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: outfile.inforesidue</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Code Short Mnemonic             Charge     MolWt Properties                     Ambiguity
A    Ala   alanine                 0.0   71.0788 tiny,small,aliphatic,nonpolar  A
B    Asx   aspartate/asparagine   -0.5  114.5962 small                          DN
C    Cys   cysteine                0.0  103.1388 tiny,small,nonpolar            C
D    Asp   aspartate              -1.0  115.0886 small,polar                    D
E    Glu   glutamate              -1.0  129.1155 polar                          E
F    Phe   phenylalanine           0.0  147.1766 aromatic,nonpolar              F
G    Gly   glycine                 0.0   57.0519 tiny,small,nonpolar            G
H    His   histidine              +0.5  137.1411 aromatic,polar                 H
I    Ile   isoleucine              0.0  113.1594 aliphatic,nonpolar             I
J    ---   leucine/isoleucine      0.0  113.1594 aliphatic,nonpolar             IL
K    Lys   lysine                 +1.0  128.1741 polar                          K
L    Leu   leucine                 0.0  113.1594 aliphatic,nonpolar             L
M    Met   methionine              0.0  131.1926 nonpolar                       M
N    Asn   asparagine              0.0  114.1038 small,polar                    N
O    ---   pyrrolysine            +1.0  237.3018 polar                          O
P    Pro   proline                 0.0   97.1167 small,nonpolar                 P
Q    Gln   glutamine               0.0  128.1307 polar                          Q
R    Arg   arginine               +1.0  156.1875 polar                          R
S    Ser   serine                  0.0   87.0782 tiny,small,polar               S
T    Thr   threonine               0.0  101.1051 tiny,small,polar               T
U    ---   selenocysteine          0.0  150.0388 tiny,small,nonpolar            U
V    Val   valine                  0.0   99.1326 small,aliphatic,nonpolar       V
W    Trp   tryptophan              0.0  186.2132 aromatic,nonpolar              W
X    Xaa   unknown                 0.0  118.8860 (none)                         ACDEFGHIKLMNPQRSTVWY
Y    Tyr   tyrosine                0.0  163.1760 aromatic,nonpolar              Y
Z    Glx   glutamate/glutamine    -0.5  128.6231 polar                          EQ
</pre>
</td></tr></table><p>





<H2>
    Data files
</H2>

<b>inforesidue</b> reads the Eresidues.iub file to define IUB standard codes
for nucleotides and ambiguity codes, and files Eamino.dat and
Emolwt.dat to read other amino acid residue chemical proerties and
molecular weights.

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

<p>

To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:

<pre>

% embossdata -fetch -file Exxx.dat

</pre>
<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>
<p>










<H2>
    Notes
</H2>

<!-- 
        Restrictions.
        Interesting behaviour.
        Useful things you can do with this program.
   -->

None.







<H2>
    References
</H2>

<!-- 
        Bibliography for methods used.
<ol>

<li>

</ol>

   -->

None.








<H2>
    Warnings
</H2>

<!-- 
        Potentially stupid things the program will let you do.
   -->

None.







<H2>
    Diagnostic Error Messages
</H2>

<!-- 
        Error messages specific to this program, eg:
        "FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
   -->

None.







<H2>
    Exit status
</H2>

<!-- 
        Description of the exit status for various error conditions
   -->

It always exits with status 0.








<H2>
    Known bugs
</H2>


<!-- 
        Bugs noted but not yet fixed.
   -->

None.








<!--
<H2>
    See also
</H2>
-->
<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="infobase.html">infobase</a></td>
<td>Return information on a given nucleotide base</td>
</tr>

</table>
<!-- 
        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
   -->










<H2>
    Author(s)
</H2>

Jon Ison
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.



<H2>
    History
</H2>
<!--
        Date written and what changes have been made go in this file.
   -->




<H2>
    Target users
</H2>
<!--
        For general users, use this text
   -->
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
<!--
        User/developer/other comments go in this file.
   -->
None


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