                                printsextract



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Extract data from PRINTS database for use by pscan

Description

   printsextract preprocesses the PRINTS database for use with the program
   pscan. It derives matrix information from the final motif sets of the
   PRINTS data file (prints.dat). 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.

Usage

   Here is a sample session with printsextract


% printsextract
Extract data from PRINTS database for use by pscan
PRINTS database file: prints.test


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

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


Input file format

  Input files for usage example

  File: prints.test

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 -> 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).


  [Part of this file has been deleted for brevity]

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;

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

   The PRINTS database is currently available via the anonymous ftp
   servers at:
     * Manchester ftp://bioinf.man.ac.uk/pub/prints/
     * EBI ftp://ftp.ebi.ac.uk/pub/databases/
     * EMBL ftp://ftp.embl-heidelberg.de/
     * NCBI ftp://ncbi.nlm.nih.gov/

   It is also distributed on the EMBL CD-ROMs.

   The home page for PRINTS is:
   http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/

Output file format

  Output files for usage example

  Directory: PRINTS

   This directory contains output files.

   The output files are held in the PRINTS subdirectory of the EMBOSS data
   directory.
     * prints.mat matrices calculated from PRINTS
     * Pxxxxx text information for each fingerprint

Data files

   None.

Notes

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

References

    1. 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.
    2. 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.
    3. 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.
    4. Attwood, T.K. and Beck, M.E. (1994) PRINTS - A protein motif
       fingerprint database. Protein Engineering, 7(7), 841-848.
    5. 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.
    6. Bleasby, A.J. and Wootton, J.C. (1990) Constructing validated, non-
       redundant composite protein sequence databases. Protein
       Engineering, 3(3), 153-159.
    7. Parry-Smith, D.J. and Attwood, T.K. (1992) ADSP - A new package for
       computational sequence analysis. CABIOS, 8(5), 451-459.
    8. Attwood, T.K. and Findlay, J.B.C. (1994) Fingerprinting
       G-protein-coupled receptors. Prot.Engng. 7(2), 195-203.
    9. 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.
   10. 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.
   11. Parry-Smith, D.J. and Attwood, T.K. (1991) SOMAP - A novel
       interactive approach to multiple protein sequence aligment. CABIOS,
       7(2), 233-235.
   12. Perkins, D.N. and Attwood, T.K. (1995) VISTAS - A package for
       VIsualising STructures And Sequences of proteins. J.Mol.Graph., 13,
       73-75.
   13. 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.

Warnings

   The program will warn you if the input file is incorrectly formatted.

   If you do not have write-access to the EMBOSS data directory, you
   should ask your system manager to run this program.

Diagnostic Error Messages

   None.

Exit status

   It exits with status 0 unless an error is reported.

Known bugs

   None.

See also

   Program name     Description
   aaindexextract   Extract amino acid property data from AAINDEX
   cutgextract      Extract codon usage tables from CUTG database
   jaspextract      Extract data from JASPAR
   prosextract      Process the PROSITE motif database for use by patmatmotifs
   rebaseextract    Process the REBASE database for use by restriction enzyme
                    applications
   tfextract        Process TRANSFAC transcription factor database for use by
                    tfscan

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Completed 8th April 1999

Target users

   This program is intended to be used by administrators responsible for
   software and database installation and maintenance.

Comments

   None
