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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: aaindexextract
  </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">
aaindexextract
</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>
Extract amino acid property data from AAINDEX
<H2>
    Description
</H2>
<p><b>aaindexextract</b> extracts amino acid property data from the <tt>AAINDEX</tt> database (see references 1, 2 and 3).  One file for every amino acid property is created in the EMBOSS data directory <tt>data/AAINDEX</tt>.  Each file corresponds to a single entry in the file <tt>aindex1</tt> of the AAINDEX database.</p>
<p>The <b>aaindexextract</b> output files files may be used by any program that uses amino acid property data.  For example, <b>pepwindow</b> and <b>pepwindowall</b> will take any one of these files if their <tt>-data</tt> qualifier is set to an appropriate file name.  By default however these programs will use the standard EMBOSS data file <tt>Enakai.dat</tt>.</p>


<H2>
    Usage
</H2>

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

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

% <b>aaindexextract </b>
Extract amino acid property data from AAINDEX
AAINDEX database file: <b>aaindex1.test</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>
Extract amino acid property data from AAINDEX
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     AAINDEX database file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   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>
</table>
<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>[-infile]<br>(Parameter 1)</td>
<td>infile</td>
<td>AAINDEX database file</td>
<td>Input file</td>
<td><b>Required</b></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>
<td colspan=5>(none)</td>
</tr>

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

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

<H2>
    Input file format
</H2>

The AAINDEX database file 'aaindex1' can be downloaded from the AAINDEX
site: 
<a href="ftp://ftp.genome.ad.jp/pub/db/community/aaindex/aaindex1">ftp://ftp.genome.ad.jp/pub/db/community/aaindex/</a>

<p>


<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: aaindex1.test</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
H CHOP780101
D Normalized frequency of beta-turn (Chou-Fasman, 1978a)
R LIT:2004003a PMID:354496
A Chou, P.Y. and Fasman, G.D.
T Empirical predictions of protein conformation
J Ann. Rev. Biochem. 47, 251-276 (1978)
C PALJ810106    0.977  TANS770110    0.956  CHAM830101    0.946
  CHOP780203    0.940  CHOP780216    0.929  CHOP780210    0.921
  ROBB760113    0.907  GEIM800108    0.899  QIAN880133    0.897
  QIAN880132    0.896  LEVM780103    0.893  PRAM900104    0.891
  LEVM780106    0.890  ROBB760108    0.887  BEGF750103    0.885
  ISOY800103    0.885  CRAJ730103    0.882  GEIM800111    0.878
  PALJ810105    0.868  ROBB760110    0.863  NAGK730103    0.827
  QIAN880131    0.824  AURR980114   -0.803  BEGF750101   -0.803
  QIAN880107   -0.809  KANM800103   -0.824  AURR980109   -0.837
  SUEM840101   -0.845
I   A/L    R/K    N/M    D/F    C/P    Q/S    E/T    G/W    H/Y    I/V
    0.66   0.95   1.56   1.46   1.19   0.98   0.74   1.56   0.95   0.47
    0.59   1.01   0.60   0.60   1.52   1.43   0.96   0.96   1.14   0.50
//
H CHOP780201
D Normalized frequency of alpha-helix (Chou-Fasman, 1978b)
R PMID:364941
A Chou, P.Y. and Fasman, G.D.
T Prediction of the secondary structure of proteins from their amino
  acid sequence
J Adv. Enzymol. 47, 45-148 (1978)
C PALJ810102    0.981  ROBB760101    0.969  ISOY800101    0.959
  KANM800101    0.956  MAXF760101    0.956  TANS770101    0.947
  BURA740101    0.917  GEIM800101    0.912  KANM800103    0.912
  LEVM780104    0.886  NAGK730101    0.886  PALJ810101    0.881
  QIAN880106    0.874  LEVM780101    0.873  PRAM900102    0.873
  GEIM800104    0.868  RACS820108    0.868  AURR980108    0.867
  AURR980109    0.859  AURR980112    0.856  CRAJ730101    0.851
  QIAN880107    0.843  BEGF750101    0.841  QIAN880105    0.835
  AURR980114    0.828  AURR980115    0.816  AURR980110    0.814
  PALJ810109    0.814  AURR980111    0.813  ROBB760103    0.806
  MUNV940101   -0.802  CRAJ730103   -0.808  ROBB760113   -0.811
  MUNV940102   -0.812  CHAM830101   -0.828  NAGK730103   -0.837
I   A/L    R/K    N/M    D/F    C/P    Q/S    E/T    G/W    H/Y    I/V
    1.42   0.98   0.67   1.01   0.70   1.11   1.51   0.57   1.00   1.08
    1.21   1.16   1.45   1.13   0.57   0.77   0.83   1.08   0.69   1.06
//
H CHOP780202
D Normalized frequency of beta-sheet (Chou-Fasman, 1978b)
R PMID:364941
A Chou, P.Y. and Fasman, G.D.
T Prediction of the secondary structure of proteins from their amino
  acid sequence
J Adv. Enzymol. 47, 45-148 (1978)


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

C ROBB760111    0.825
I   A/L    R/K    N/M    D/F    C/P    Q/S    E/T    G/W    H/Y    I/V
    0.058  0.085  0.091  0.081  0.128  0.098  0.064  0.152  0.054  0.056
    0.070  0.095  0.055  0.065  0.068  0.106  0.079  0.167  0.125  0.053
//
H CHOP780216
D Normalized frequency of the 2nd and 3rd residues in turn (Chou-Fasman, 1978b)
R PMID:364941
A Chou, P.Y. and Fasman, G.D.
T Prediction of the secondary structure of proteins from their amino
  acid sequence
J Adv. Enzymol. 47, 45-148 (1978)
C CHOP780203    0.979  GEIM800111    0.955  LEVM780106    0.953
  LEVM780103    0.952  PRAM900104    0.951  CHAM830101    0.942
  GEIM800108    0.942  QIAN880133    0.939  QIAN880132    0.931
  TANS770110    0.930  CHOP780101    0.929  ISOY800103    0.921
  PALJ810106    0.904  QIAN880134    0.900  CHOP780210    0.896
  QIAN880135    0.884  PALJ810105    0.881  QIAN880131    0.873
  NAGK730103    0.819  QIAN880120   -0.800  FAUJ880102   -0.807
  KANM800103   -0.808  QIAN880107   -0.808  ROBB760103   -0.841
  PTIO830101   -0.855  SUEM840101   -0.874
I   A/L    R/K    N/M    D/F    C/P    Q/S    E/T    G/W    H/Y    I/V
    0.64   1.05   1.56   1.61   0.92   0.84   0.80   1.63   0.77   0.29
    0.36   1.13   0.51   0.62   2.04   1.52   0.98   0.48   1.08   0.43
//
H KYTJ820101
D Hydropathy index (Kyte-Doolittle, 1982)
R LIT:0807099 PMID:7108955
A Kyte, J. and Doolittle, R.F.
T A simple method for displaying the hydropathic character of a protein
J J. Mol. Biol. 157, 105-132 (1982)
C CHOC760103    0.964  JANJ780102    0.922  DESM900102    0.898
  EISD860103    0.897  CHOC760104    0.889  WOLR810101    0.885
  RADA880101    0.884  MANP780101    0.881  EISD840101    0.878
  PONP800103    0.870  NAKH920108    0.868  JANJ790101    0.867
  JANJ790102    0.866  PONP800102    0.861  MEIH800103    0.856
  PONP800101    0.851  PONP800108    0.850  WARP780101    0.845
  RADA880108    0.842  ROSG850102    0.841  DESM900101    0.837
  BIOV880101    0.829  RADA880107    0.828  CIDH920104    0.824
  KANM800104    0.824  LIFS790102    0.824  MIYS850101    0.821
  RADA880104    0.819  NAKH900111    0.817  NISK800101    0.812
  FAUJ830101    0.811  ARGP820103    0.806  ARGP820102    0.803
  NAKH920105    0.803  KRIW790101   -0.805  CHOC760102   -0.838
  MONM990101   -0.842  GUYH850101   -0.843  RACS770102   -0.844
  JANJ780103   -0.845  ROSM880101   -0.845  PRAM900101   -0.850
  JANJ780101   -0.852  GRAR740102   -0.859  MEIH800102   -0.871
  ROSM880102   -0.878  OOBM770101   -0.899
I   A/L    R/K    N/M    D/F    C/P    Q/S    E/T    G/W    H/Y    I/V
    1.8   -4.5   -3.5   -3.5    2.5   -3.5   -3.5   -0.4   -3.2    4.5
    3.8   -3.9    1.9    2.8   -1.6   -0.8   -0.7   -0.9   -1.3    4.2
//
</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>

One file for every entry in the AAINDEX database is created in the
EMBOSS standard 'data/AAINDEX' directory.  For example, the file
'kytj820101':

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>Directory: AAINDEX</h3>
<p>This directory contains output files, for example kytj820101.
<p><h3>File: AAINDEX/kytj820101</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
H KYTJ820101
D Hydropathy index (Kyte-Doolittle, 1982)
R LIT:0807099 PMID:7108955
A Kyte, J. and Doolittle, R.F.
T A simple method for displaying the hydropathic character of a protein
J J. Mol. Biol. 157, 105-132 (1982)
C CHOC760103    0.964  JANJ780102    0.922  DESM900102    0.898
  EISD860103    0.897  CHOC760104    0.889  WOLR810101    0.885
  RADA880101    0.884  MANP780101    0.881  EISD840101    0.878
  PONP800103    0.870  NAKH920108    0.868  JANJ790101    0.867
  JANJ790102    0.866  PONP800102    0.861  MEIH800103    0.856
  PONP800101    0.851  PONP800108    0.850  WARP780101    0.845
  RADA880108    0.842  ROSG850102    0.841  DESM900101    0.837
  BIOV880101    0.829  RADA880107    0.828  CIDH920104    0.824
  KANM800104    0.824  LIFS790102    0.824  MIYS850101    0.821
  RADA880104    0.819  NAKH900111    0.817  NISK800101    0.812
  FAUJ830101    0.811  ARGP820103    0.806  ARGP820102    0.803
  NAKH920105    0.803  KRIW790101   -0.805  CHOC760102   -0.838
  MONM990101   -0.842  GUYH850101   -0.843  RACS770102   -0.844
  JANJ780103   -0.845  ROSM880101   -0.845  PRAM900101   -0.850
  JANJ780101   -0.852  GRAR740102   -0.859  MEIH800102   -0.871
  ROSM880102   -0.878  OOBM770101   -0.899
I   A/L    R/K    N/M    D/F    C/P    Q/S    E/T    G/W    H/Y    I/V
    1.8   -4.5   -3.5   -3.5    2.5   -3.5   -3.5   -0.4   -3.2    4.5
    3.8   -3.9    1.9    2.8   -1.6   -0.8   -0.7   -0.9   -1.3    4.2
//
</pre>
</td></tr></table><p>


<H2>
    Data files
</H2>

None.

<H2>
    Notes
</H2>
<p>AAINDEX is a database of  biochemical and physicochemical properties of amino acids and pairs of amino acids. <tt>aaindex1</tt> for properties of each of the 20 single amino acids, <tt>aaindex2</tt> for amino acid mutation matrices and <tt>aaindex3</tt> for the amino-acid pair-wise contact potentials. All data are derived from the published literature.  The file <tt>aaindex1</tt> is required by <b>aaindexextract</b> and can be downloaded from the AAINDEX site: <a href="ftp://ftp.genome.ad.jp/pub/db/community/aaindex/aaindex1">ftp://ftp.genome.ad.jp/pub/db/community/aaindex/aaindex1</a>.</p>

<p><b>aaindexextract</b> will write to the EMBOSS data directory <tt>data/AAINDEX</tt>.  If you cannot find the output files then it is likely the data directory has been set to somewhere other than expected.  To set explicitly the location of the EMBOSS data directory add the following to your <tt>emboss.default</tt> file:</p>

<p><tt>ENV EMBOSS_DATA /path/to/the/EMBOSS/data/directory</tt></p>
<p>Where <tt>/path/to/the/EMBOSS/data/directory</tt> is the location of your EMBOSS data as unpacked from the distribution file.</p>



<H2>
    References
</H2>

<ol>

<li>Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino
acid indices for prediction of protein structure and function. Protein
Eng. 2, 93-100 (1988). [UI:<A
href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&dopt=r&uid=3244698">89221001</a>]

<li>Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and
mutation matrices for sequence comparison and structure prediction of
proteins. Protein Eng. 9, 27-36 (1996). [UI:<a
href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&dopt=r&uid=9053899">96272030</a>]

<li>Kawashima, S., Ogata, H., and Kanehisa, M.; AAindex: amino acid
index database. Nucleic Acids Res. 27, 368-369 (1999). [UI:<a
href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&dopt=r&uid=9847231">99063742</a>]

</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="cutgextract.html">cutgextract</a></td>
<td>Extract codon usage tables from CUTG database</td>
</tr>

<tr>
<td><a href="jaspextract.html">jaspextract</a></td>
<td>Extract data from JASPAR</td>
</tr>

<tr>
<td><a href="printsextract.html">printsextract</a></td>
<td>Extract data from PRINTS database for use by pscan</td>
</tr>

<tr>
<td><a href="prosextract.html">prosextract</a></td>
<td>Process the PROSITE motif database for use by patmatmotifs</td>
</tr>

<tr>
<td><a href="rebaseextract.html">rebaseextract</a></td>
<td>Process the REBASE database for use by restriction enzyme applications</td>
</tr>

<tr>
<td><a href="tfextract.html">tfextract</a></td>
<td>Process TRANSFAC transcription factor database for use by tfscan</td>
</tr>

</table>

<p>
The programs 
<a href="pepwindow.html">pepwindow</a>
and
<a href="pepwindowall.html">pepwindowall</a>
normally use the standard EMBOSS data file 'Enakai.dat' by default, but
you can set their '-data' qualifier to use any of the files produced by
<b>aaextractindex</b>. 

<H2>
    Author(s)
</H2>

Peter Rice
<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>


Written (25 June 2002) - Peter Rice


<H2>
    Target users
</H2>
This program is intended to be used by administrators responsible
for software and database installation and maintenance. 
<H2>
    Comments
</H2>
None


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