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EMBOSS: printsextract
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Program printsextract
Function
Extract data from PRINTS
Description
Preprocesses the PRINTS database for use with the program PSCAN.
This program 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
Full pathname of PRINTS.DAT: /data/prints/prints.dat
Command line arguments
Mandatory qualifiers:
[-inf] infile Full pathname of prints.dat
Optional qualifiers: (none)
Advanced qualifiers: (none)
General qualifiers:
-help bool report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
|
Mandatory qualifiers |
Allowed values |
Default |
[-inf] (Parameter 1) |
Full pathname of prints.dat |
Input file |
Required |
Optional qualifiers |
Allowed values |
Default |
(none) |
Advanced qualifiers |
Allowed values |
Default |
(none) |
Input file format
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:
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
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
- embossre.sup Enzyme suppliers
Data files
The "prints.dat" file of a PRINTS distribution is the input file for this
program.
Notes
You may have to ask your system manager to run this program.
References
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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.
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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.
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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.
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Attwood, T.K. and Beck, M.E. (1994) PRINTS - A protein motif fingerprint
database. Protein Engineering, 7(7), 841-848.
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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.
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Bleasby, A.J. and Wootton, J.C. (1990) Constructing validated, non-
redundant composite protein sequence databases. Protein Engineering, 3(3),
153-159.
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Parry-Smith, D.J. and Attwood, T.K. (1992) ADSP - A new package for
computational sequence analysis. CABIOS, 8(5), 451-459.
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Attwood, T.K. and Findlay, J.B.C. (1994) Fingerprinting G-protein-coupled
receptors. Prot.Engng. 7(2), 195-203.
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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.
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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.
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Parry-Smith, D.J. and Attwood, T.K. (1991) SOMAP - A novel interactive
approach to multiple protein sequence aligment. CABIOS, 7(2), 233-235.
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Perkins, D.N. and Attwood, T.K. (1995) VISTAS - A package for VIsualising
STructures And Sequences of proteins. J.Mol.Graph., 13, 73-75.
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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.
Diagnostic Error Messages
None.
Exit status
It exits with status 0 unless an error is reported.
Known bugs
None.
Program name | Description |
cutgextract | Extract data from CUTG |
domainer | Build domain coordinate files |
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one |
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scope | Convert raw scop classification file to embl-like format |
scopparse | Reads raw scop classifications file and writes embl-like format scop classification file |
seqnr | Converts redundant database results to a non-redundant set of hits |
tfextract | Extract data from TRANSFAC |
Author(s)
This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
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