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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="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>
<p>
<H2>
Function
</H2>
Extract data from AAINDEX
<H2>
Description
</H2>
<b>aaextractindex</b> extracts information from the AAINDEX database for use by
<a href="pepwindow.html">pepwindow</a>
and
<a href="pepwindowall.html">pepwindowall</a>
<p>
AAINDEX is a database of properties of amino acids. See references [1] [2] [3].
<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> from the AAINDEX database.
<p>
The AAINDEX database file 'aaindex1' can be downloaded from the AAINDEX
site:
<a href="ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1">ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1</a>
<H2>
Usage
</H2>
<b>Here is a sample session with aaindexextract</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>aaindexextract </b>
Extract 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>
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 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>
</table>
<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>[-infile]<br>(Parameter 1)</td>
<td>AAINDEX database file</td>
<td>Input file</td>
<td><b>Required</b></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 colspan=4>(none)</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 colspan=4>(none)</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/genomenet/aaindex/aaindex1">ftp://ftp.genome.ad.jp/pub/db/genomenet/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>
If <b>aaindexextract</b> tries to write the data to an unexpected
location you can explicitly set the location of the EMBOSS data
directory by putting the line:
<p>
ENV EMBOSS_DATA /path/to/the/EMBOSS/data/directory
<br>
in the EMBOSS <b>emboss.default</b> file.
<p>
(Where '/path/to/the/EMBOSS/data/directory' is the location of your
EMBOSS data as unpacked from the distribution file.)
<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 data from CUTG</td>
</tr>
<tr>
<td><a href="printsextract.html">printsextract</a></td>
<td>Extract data from PRINTS</td>
</tr>
<tr>
<td><a href="prosextract.html">prosextract</a></td>
<td>Build the PROSITE motif database for use by patmatmotifs</td>
</tr>
<tr>
<td><a href="rebaseextract.html">rebaseextract</a></td>
<td>Extract data from REBASE</td>
</tr>
<tr>
<td><a href="tfextract.html">tfextract</a></td>
<td>Extract data from TRANSFAC</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 (pmr © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<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
</BODY>
</HTML>
|
