EMBOSS: printsextract


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)

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.

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

  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.

Diagnostic Error Messages

None.

Exit status

It exits with status 0 unless an error is reported.

Known bugs

None.

See also

Program nameDescription
embossdataFinds or fetches the data files read in by the EMBOSS programs
helixturnhelixReport nucleic acid binding motifs
patmatdbSearch a protein sequence with a motif
patmatmotifsSearch a PROSITE motif database with a protein sequence
prosextractBuilds the PROSITE motif database for patmatmotifs to search
pscanScans proteins using PRINTS
rebaseextractExtract data from REBASE
tfextractExtract data from TRANSFAC
tfscanScans DNA sequences for transcription factors

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