EMBOSS: pscan

| ## 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