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<HEAD>
  <TITLE>
  EMBOSS: printsextract
  </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">
printsextract
</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 data from PRINTS database for use by pscan

<H2>
    Description
</H2>

<p><b>printsextract</b> preprocesses the PRINTS database for use with the program pscan. It derives matrix information from the final motif sets of the PRINTS data file (<tt>prints.dat</tt>). It creates files in the EMBOSS data subdirectory PRINTS these being a matrix file and files containing text information for each fingerprint. Running this program may be the job of your system manager.</p>

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

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

% <b>printsextract </b>
Extract data from PRINTS database for use by pscan
PRINTS database file: <b>prints.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 data from PRINTS database for use by pscan
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     PRINTS 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>
<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>[-infile]<br>(Parameter 1)</td>
<td>infile</td>
<td>PRINTS 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>



<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: prints.test</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
gc; ACHEFISH
gx; PR00879
gn; COMPOUND(4)
ga; 06-JUL-1998; UPDATE 06-JUN-1999
gt; Fish acetylcholinesterase signature
gp; PRINTS; PR00878 CHOLNESTRASE; PR00880 ACHEINSECT
gp; INTERPRO; IPR000908
gp; PDB; 2ACE
gp; SCOP; 2ACE
gp; CATH; 2ACE
bb;
gr; 1. VOET, D. AND VOET, J.G.
gr; Biochemical communications: Hormones and neurotransmission.
gr; BIOCHEMISTRY 34(4) 1298-1299 (1995).
gr; 
gr; 2. COUSIN, X., HOTELIER, T., GILES, K., TOUTANT, J.P. AND CHATONNET, A.
gr; aCHEdb: the database system for ESTHER, the a/b fold family of proteins and
gr; the cholinesterase gene server.
gr; NUCLEIC ACIDS RES. 26 226-228 (1998).
gr; 
gr; 3. THE ESTHER DATABASE
gr; http://meleze.ensam.inra.fr/cholinesterase/definitions.html
gr; 
gr; 4. CHOLINESTERASES
gr; http://bnlstb.bio.bnl.gov:8000/disk$3/giles/che.html
bb;
bb;
gd; Acetylcholine is involved in the transfer of messages across a variety of
gd; synapses in vertebrates and invertebrates. The diverse physiological effects
gd; attributable to this molecule arise from the presence of specific receptors
gd; in the postsynaptic cell membranes. Several classes of receptor are known, 
gd; most of which translate the binding of acetylcholine into the opening of 
gd; channels for the passage of ions, such as sodium and potassium.
gd;
gd; Acetylcholinesterase is an enzyme that catalyses the hydrolysis of 
gd; acetylcholine to choline and acetate:
gd; 
gd;	     Acetylcholine + H(2)O -&gt; Choline + Acetate 	     
gd; 
gd; The enzyme also acts on a variety of acetic esters and catalyses trans-
gd; acetylations. It is found in, or attached to, cellular or basement membranes
gd; of presynaptic cholinergic neurons and postsynaptic cholinoceptive cells.
gd; To prevent continuous firing of nerve impulses, acetylcholinesterase has a
gd; high K(cat) (~14000/s), to ensure that acetylcholine is broken down quickly.
gd;
gd; Cholinesterases constitute a family of enzymes that fall into two main
gd; types, depending on their substrate preference: enzymes that preferentially
gd; hydrolyse acetyl esters are termed acetylcholinesterase (AChE) (EC 3.1.1.7); 
gd; and those that prefer other types of ester, such as butyrylcholine are 
gd; termed butyrylcholinesterase (BChE) (EC 3.1.1.8). 


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

fd; YFISGFLFYLATIINPIAYNLASSRFR          Q18701    323    17
fd; FIISMLLASLNSCCNPWIYMFFAGHLF          Q90334    311    13
fd; YKITRPLASANSCLDPVLYFLAGQRLV        P2UR_RAT    287    20
fd; AAMPAYFAKSATIYNPIIYVFMNRQFR      OPSR_CARAU    301    13
fd; AQWFIVLAVLNSAMNPVIYTLASKEMR      EDG3_HUMAN    280    14
fd; YKVTRPLASANSCLDPVLYFLAGQRLV      P2UR_HUMAN    288    20
fd; YKITRPLASANSCLDPVLYFLAGQRLV      P2UR_MOUSE    288    20
fd; AAMPAYFAKSATIYNPVIYVFMNRQFR      OPSR_ORYLA    301    13
fd; MAIPSFFSKSSALFNPIIYILLNKQFR      OPSG_ORYLA    289    13
fd; THFAFALQYINSAANPFLYVFLSDSFQ          Q23033    401    16
fd; FTAITWISFSSSASKPTLYSIYNANFR      GPRJ_HUMAN    312    13
fd; AALPAYFAKSATIYNPIIYVFMNRQFR      OPSR_CAPHI    304    13
fd; YINIYWLGMSSTVFNPVIYYFMNKRFR          O44148    323    16
fd; LHFTVCLMNFNCCMDPFIYFFACKGYK      EBI2_HUMAN    290    23
fd; FTAVTWVSFSSSASKPTLYSIYNANFR      GPRJ_MOUSE    306    13
fd; NYTGINMASLNSCIGPVALYFVSRKFK      ET3R_XENLA    365    36
fd; TIWGSVFAKANSCYNPIVYGISHPRYK      OPS2_LIMPO    310    13
fd; YLVALCLSTLNSCIDPFVYYFVSKDFR      PAR2_MOUSE    328    16
fd; YIVALCLSTLNSCIDPFVYYFVSHDFR      PAR2_HUMAN    326    16
fd; YLVALCLSTLNSCIDPFVYYFVSKDFR        PAR2_RAT    326    16
fd; YILSACVGSVSCCLDPLIYYYASSQCQ      THRR_XENLA    348    13
fd; TIWGSVFAKANAVYNPIVYGISHPKYR          O76125    317    12
fd; TIWGSVFAKANSCYNPIVYGISHPRYK      OPS1_LIMPO    310    13
fd; YLIALCLGSLNSCLDPFLYFVMSKVVD      PAR3_MOUSE    339    16
fd; TIWGSVFAKANAVYNPIVYGISHPKYR          O76123    317    12
fd; YLLCVCVTSVASCIDPLIYYYASSECQ        THRR_RAT    360    17
fd; VHVAEIVSLCHCFINPLIYAFCSREFT      VQ3L_CAPVK    337    21
fd; TIWGSLFAKANAVFNPIVYGISHPKYR      OPS1_SCHGR    315    12
fd; AAAPAFFSKTAAVYNPVIYVFMNKQVS      OPSO_SALSA    286    13
fd; YHFSLLLTSFNCVADPVLYCFVSETTH          O46685    268    17
fd; KILLVLFYPINSCANPFLYAIFTKNFR      FSHR_HORSE    607    13
fd; YIFCHLVGISSTCVNPIVYALVNESFR          O44690    308    12
fd; YLLCVCVSSISSCIDPLIYYYASSECQ      THRR_HUMAN    353    17
fd; AALPAYFAKSATIYNPIIYVFMNRQFR      OPSR_XENLA    303    13
fd; ITFSETISLARCCINPIIYTLIGEHVR      VK02_SPVKA    312    24
fd; YHSSLAFTSLNCVADPILYCLVNEGAR      GPR4_HUMAN    268    21
fd; YHFSLLLTSFNCVADPVLYCFVSETTH      OGR1_HUMAN    268    17
fd; YHSSLAFTSLNCVADPILYCLVNEGAR        GPR4_PIG    268    21
fd; TIWGSLFAKANAVYNPIVYGISHPKYR      OPSD_CAMAB    315    12
fd; TIWGSLFAKANAVYNPIVYGISHPKYR      OPSD_CATBO    315    12
fd; KILLVFFYPLNSCADPYLYAILTSQYR          Q94979    738    13
fd; TIWGACFAKSAACYNPIVYGISHPKYG      OPS1_CALVI    309    12
fd; KILLVLFYPINSCANPFLYAIFTKTFR      FSHR_CHICK    608    13
fd; KILLVLFYPINSCANPFLYAIFTKNFR      FSHR_EQUAS    600    13
fd; TMLPAVFAKTVSCIDPWIYAINHPRYR      OPSB_APIME    318    13
fd; TMIPAVTAKIVSCIDPWVYAINHPRFR      OPS2_SCHGR    315    13
fd; TIWGACFAKSAACYNPIVYGISHPKYR      OPS1_DROME    311    12
fd; TIWGSLFAKANAVYNPIVYGISHPKYR      OPSD_APIME    313    12
fd; SMLPCLACKSVSCLDPWVYATSHPKYR      OPS5_DROME    314    13
fd; TICGSVFAKANAVCNPIVYGLSHPKYK      OPS6_DROME    309    12
bb;
</pre>
</td></tr></table><p>

<p>

The input file must be the "prints.dat" file of a PRINTS distribution. 

<p>
The PRINTS database is currently available via the anonymous ftp servers at: 

<ul>

<li>  Manchester   <a href="ftp://bioinf.man.ac.uk/pub/prints/">ftp://bioinf.man.ac.uk/pub/prints/</a>
<li>  EBI          <a href="ftp://ftp.ebi.ac.uk/pub/databases/">ftp://ftp.ebi.ac.uk/pub/databases/</a>
<li>  EMBL         <a href="ftp://ftp.embl-heidelberg.de/">ftp://ftp.embl-heidelberg.de/</a>
<li>  NCBI         <a href="ftp://ncbi.nlm.nih.gov/">ftp://ncbi.nlm.nih.gov/</a>

</ul>

<p>
It is also distributed on the EMBL CD-ROMs. 
<p>

The home page for PRINTS is: <a
href="http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/">http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/</a>

<H2>
    Output file format
</H2>



<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>Directory: PRINTS</h3>
<p>This directory contains output files.
<p>

<p>

The output files are held in the PRINTS subdirectory of the EMBOSS data
directory.

<ul>
	<li> prints.mat		matrices calculated from PRINTS
	<li> Pxxxxx		text information for each fingerprint
</ul>

<H2>
    Data files
</H2>


None.

<H2>
    Notes
</H2>

You may have to ask your system manager to run this program.


<H2>
    References
</H2>


<ol>

<li>
 Attwood, T.K., Flower, D.R., Lewis, A.P., Mabey, J.E., Morgan, S.R., 
   Scordis, P., Selley, J. and Wright, W. (1999) PRINTS prepares for the new
   millennium. Nucleic Acids Research, 27(1), 220-225. 

<li>
 Attwood, T.K., Beck, M.E., Flower, D.R., Scordis, P. and Selley, J. (1998)
   The PRINTS protein fingerprint database in its fifth year. Nucleic Acids 
   Research, 26(1), 304-308. 

<li>
 Attwood, T.K., Beck, M.E., Bleasby, A.J., Degtyarenko, K., Michie, A.D. and 
   Parry-Smith, D.J. (1997) Novel developments with the PRINTS protein motif
   fingerprint database. Nucleic Acids Research, 25 (1), 212-216.

<li>
 Attwood, T.K. and Beck, M.E. (1994) PRINTS - A protein motif fingerprint
   database. Protein Engineering, 7(7), 841-848.

<li>
 Bleasby, A.J., Akrigg, D.A. and Attwood, T.K. (1994) OWL - A non-redundant
   composite protein sequence database. Nucleic Acids Research, 22(17), 3574-77.

<li>
Bleasby, A.J. and Wootton, J.C. (1990) Constructing validated, non-
   redundant composite protein sequence databases. Protein Engineering, 3(3), 
   153-159. 

<li>
Parry-Smith, D.J. and Attwood, T.K. (1992) ADSP - A new package for
   computational sequence analysis. CABIOS, 8(5), 451-459.

<li>
Attwood, T.K. and Findlay, J.B.C. (1994) Fingerprinting G-protein-coupled
   receptors. Prot.Engng. 7(2), 195-203.

<li>
Attwood, T.K. and Findlay, J.B.C. (1993) Design of a discriminating finger-
   print for G-protein-coupled receptors. Prot.Engng. 6(2) 167-176.

<li>
 Akrigg, D., Attwood, T.K., Bleasby, A.J., Findlay, J.B.C, North, A.C.T.,
   Maughan, N.A., Parry-Smith, D.J., Perkins, D.N. and Wootton, J.C. (1992)
   SERPENT - An information storage and analysis resource for protein
   sequences. CABIOS 8(3) 295-296.

<li>
Parry-Smith, D.J. and Attwood, T.K. (1991) SOMAP - A novel interactive
    approach to multiple protein sequence aligment. CABIOS, 7(2), 233-235.

<li>
Perkins, D.N. and Attwood, T.K. (1995) VISTAS - A package for VIsualising
    STructures And Sequences of proteins. J.Mol.Graph., 13, 73-75. 

<li>
Parry-Smith, D.J., Payne, A.W.R, Michie, A.D. and Attwood, T.K. (1998) 
    CINEMA - A novel Colour INteractive Editor for Multiple Alignments.
    Gene, 211(2), GC45-56. 

</ol>

<H2>
    Warnings
</H2>
<p>The program will warn you if the input file is incorrectly formatted.</p>
<p>If you do not have write-access to the EMBOSS data directory, you should ask your system manager to run this program.</p>



<H2>
    Diagnostic Error Messages
</H2>

None.


<H2>
    Exit status
</H2>


It exits with status 0 unless an error is reported.

<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="aaindexextract.html">aaindexextract</a></td>
<td>Extract amino acid property data from AAINDEX</td>
</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="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>

<H2>
    Author(s)
</H2>


Alan Bleasby 
<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>

Completed 8th April 1999

<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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