
                               EMBOSS: pscan
     _________________________________________________________________
   
                                 Program pscan
                                       
Function

   Scans proteins using PRINTS
   
Description

   PRINTS is a database of diagnostic protein signatures, or
   fingerprints.
   
   Fingerprints are groups of conserved motifs or elements that together
   form a diagnostic signature for particular protein families.
   
   An uncharacterised sequence matching all motifs or elements can then
   be readily diagnosed as a true match to a particular family
   fingerprint.
   
   They can be used to diagnose family relationships in newly-determined
   sequences (especially from genome projects).
   
   Usually the motifs or elements do not overlap, but are separated along
   a sequence, though they may be contiguous in 3D-space. Fingerprints
   can encode protein folds and functionalities more flexibly and
   powerfully than can single motifs, full diagnostic potency deriving
   from the mutual context provided by motif neighbours.
   
   Diagnostically, this is more powerful than using single motifs by
   virtue of the biological context afforded by matching motif
   neighbours.
   
   pscan finds matches between a query protein sequence and the motifs or
   elements in the PRINTS database. It reports various classes of
   matches:
   
     * Matches where all elements of a motif exist in the correct order
     * Matches where all elements exist but some are in the incorrect
       order
     * Matches where some elements match and are in the correct order
     * Miscellaneous matches.
       
   The home web page of the PRINTS database is:
   http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
   
Usage

   Here is a sample session with pscan.

% pscan
Scans proteins using PRINTS
Input sequence(s): sw:OPSD_HUMAN
Minimum number of elements per fingerprint [2]:
Maximum number of elements per fingerprint [20]:
Output file [opsd_human.pscan]:
%

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
   -emin               integer    Minimum number of elements per fingerprint
   -emax               integer    Maximum number of elements per fingerprint
  [-outfile]           outfile    Output file name

   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
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -emin Minimum number of elements per fingerprint Integer from 1 to 20
   2
   -emax Maximum number of elements per fingerprint Integer up to 20 20
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.pscan
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   The input sequence can be one or more protein sequences.
   
Output file format

   The program reports hits in four classes.
   
   Class1:
          Matches where all elements of a motif exist in the correct
          order
          
   Class2:
          Matches where all elements exist but some are in the incorrect
          order
          
   Class3:
          Matches where some elements match and are in the correct order
          
   Class4:
          Miscellaneous matches
          
   Here is part of a sample output:

CLASS 1
Fingerprints with all elements in order

Fingerprint GPCRRHODOPSN Elements 7
    Accession number PR00237
    Rhodopsin-like GPCR superfamily signature
  Element 1 Threshold 54% Score 64%
             Start position 39 Length 25
  Element 2 Threshold 49% Score 75%
             Start position 72 Length 22
  Element 3 Threshold 48% Score 56%
             Start position 117 Length 23
  Element 4 Threshold 50% Score 69%
             Start position 152 Length 22
  Element 5 Threshold 51% Score 74%
             Start position 204 Length 24
  Element 6 Threshold 42% Score 75%
             Start position 250 Length 25
  Element 7 Threshold 46% Score 67%
             Start position 288 Length 27


CLASS 2
All elements match but not all in the correct order

Fingerprint RHODOPSIN Elements 6
    Accession number PR00579
    Rhodopsin signature
  Element 1 Threshold 80% Score 96%
             Start position 3 Length 19
  Element 2 Threshold 76% Score 100%
             Start position 22 Length 17
  Element 3 Threshold 53% Score 92%
             Start position 85 Length 17
  Element 4 Threshold 71% Score 100%
             Start position 191 Length 17
  Element 5 Threshold 56% Score 99%
             Start position 271 Length 19
  Element 6 Threshold 81% Score 93%
             Start position 319 Length 14


CLASS 3
Not all elements match but those that do are in order

Fingerprint PROFILIN Elements 6
    Accession number PR00392
    Profilin signature
  Element 6 Threshold 31% Score 31%
             Start position 18 Length 18
  Element 6 Threshold 37% Score 37%
             Start position 318 Length 15


CLASS 4
Remaining partial matches

Fingerprint NANEUSMPORT Elements 8
    Accession number PR00176
    Sodium/chloride neurotransmitter symporter signature
  Element 2 Threshold 47% Score 47%
             Start position 38 Length 20

Data files

   The data file is stored in the PRINTS directory of the standard EMBOSS
   data directory.
     * prints.mat Matrices derived from PRINTS
     * Pxxxxx Information for each fingerprint
       
   The column information is described at the top of the matrix data file
   
Notes

   The matrix information used to scan a sequence is derived from the
   final motif sets in the PRINTS database. The matrices are of the
   simple frequency type and contain the number of times a residue occurs
   in each position of the alignment. Each matrix therefore has a highest
   possible score, being the sum of the maximum score of each column. A
   match to the sequence window is obtained if it has a score equal to or
   greater than the percentage of the maximum score of the lowest scoring
   sequence in the final motif set.
   
   The data files must have been created before running this program.
   This is done by running the printsextract program with the
   "prints.dat" file from a PRINTS release. You may have to ask your
   system manager to do this.
   
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 a DNA sequence is given.
   
Diagnostic Error Messages

   If you get the following EMBOSS FATAL ERROR message:

"prints.mat file not found. Create it with printsextract."

   then your local PRINTS data has not been set up correctly in your
   EMBOSS DATA directory. Use 'printsextract' to do this.
   
Exit status

   It exits with status 0 unless an error is reported.
   
Known bugs

See also

    Program name                        Description
   antigenic      Finds antigenic sites in proteins
   digest         Protein proteolytic enzyme or reagent cleavage digest
   fuzzpro        Protein pattern search
   fuzztran       Protein pattern search after translation
   helixturnhelix Report nucleic acid binding motifs
   oddcomp        Finds protein sequence regions with a biased composition
   patmatdb       Search a protein sequence with a motif
   patmatmotifs   Search a PROSITE motif database with a protein sequence
   pepcoil        Predicts coiled coil regions
   preg           Regular expression search of a protein sequence
   sigcleave      Reports protein signal cleavage sites
   
     * printsextract - Extract data from PRINTS. pscan uses the PRINTS
       data. Until printsextract has been run to set up the PRINTS data,
       pscan will not run correctly.
       
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
