| 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): tsw:opsd_human
    Minimum number of elements per fingerprint [2]:
    Maximum number of elements per fingerprint [20]:
    Output file [opsd_human.pscan]:

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

## 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)
       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -sreverse1           boolean    Reverse (if DNA)
       -sask1               boolean    Ask for begin/end/reverse
       -snucleotide1        boolean    Sequence is nucleotide
       -sprotein1           boolean    Sequence is protein
       -slower1             boolean    Make lower case
       -supper1             boolean    Make upper case
       -sformat1            string     Input sequence format
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outfile" related qualifiers
       -odirectory2         string     Output directory

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -verbose             boolean    Report some/full command line options
       -help                boolean    Report command line options. 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 deaths

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

pscan reads one or more protein sequence USAs.

### Input files for usage example

'tsw:opsd_human' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:opsd_human

    ID   OPSD_HUMAN     STANDARD;      PRT;   348 AA.
    AC   P08100; Q16414;
    DT   01-AUG-1988 (Rel. 08, Created)
    DT   01-AUG-1988 (Rel. 08, Last sequence update)
    DT   15-JUL-1999 (Rel. 38, Last annotation update)
    DE   RHODOPSIN.
    GN   RHO.
    OS   Homo sapiens (Human).
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
    OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
    RN   [1]
    RP   SEQUENCE FROM N.A.
    RX   MEDLINE; 84272729.
    RA   NATHANS J., HOGNESS D.S.;
    RT   "Isolation and nucleotide sequence of the gene encoding human
    RT   rhodopsin.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
    RN   [2]
    RP   SEQUENCE OF 1-120 FROM N.A.
    RA   BENNETT J., BELLER B., SUN D., KARIKO K.;
    RL   Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases.
    RN   [3]
    RP   REVIEW ON ADRP VARIANTS.
    RX   MEDLINE; 94004905.
    RA   AL-MAGHTHEH M., GREGORY C., INGLEHEARN C., HARDCASTLE A.,
    RA   BHATTACHARYA S.;
    RT   "Rhodopsin mutations in autosomal dominant retinitis pigmentosa.";
    RL   Hum. Mutat. 2:249-255(1993).
    RN   [4]
    RP   VARIANT ADRP HIS-23.
    RX   MEDLINE; 90136922.
    RA   DRYJA T.P., MCGEE T.L., REICHEI E., HAHN L.B., COWLEY G.S.,
    RA   YANDELL D.W., SANDBERG M.A., BERSON E.L.;
    RT   "A point mutation of the rhodopsin gene in one form of retinitis
    RT   pigmentosa.";
    RL   Nature 343:364-366(1990).
    RN   [5]
    RP   VARIANTS ADRP.
    RX   MEDLINE; 91051574.
    RA   FARRAR G.J., KENNA P., REDMOND R., MCWILLIAM P., BRADLEY D.G.,
    RA   HUMPHRIES M.M., SHARP E.M., INGLEHEARN C.F., BASHIR R., JAY M.,
    RA   WATTY A., LUDWIG M., SCHINZEL A., SAMANNS C., GAL A.,
    RA   BHATTACHARYA S.S., HUMPHRIES P.;
    RT   "Autosomal dominant retinitis pigmentosa: absence of the rhodopsin
    RT   proline-->histidine substitution (codon 23) in pedigrees from
    RT   Europe.";
    RL   Am. J. Hum. Genet. 47:941-945(1990).
    RN   [6]
    RP   VARIANTS ADRP HIS-23; ARG-58; LEU-347 AND SER-347.
    RX   MEDLINE; 91015273.

      [Part of this file has been deleted for brevity]

    FT                                /FTId=VAR_004816.
    FT   VARIANT     209    209       V -> M (EFFECT NOT KNOWN).
    FT                                /FTId=VAR_004817.
    FT   VARIANT     211    211       H -> P (IN ADRP).
    FT                                /FTId=VAR_004818.
    FT   VARIANT     211    211       H -> R (IN ADRP).
    FT                                /FTId=VAR_004819.
    FT   VARIANT     216    216       M -> K (IN ADRP).
    FT                                /FTId=VAR_004820.
    FT   VARIANT     220    220       F -> C (IN ADRP).
    FT                                /FTId=VAR_004821.
    FT   VARIANT     222    222       C -> R (IN ADRP).
    FT                                /FTId=VAR_004822.
    FT   VARIANT     255    255       MISSING (IN ADRP).
    FT                                /FTId=VAR_004823.
    FT   VARIANT     264    264       MISSING (IN ADRP).
    FT                                /FTId=VAR_004824.
    FT   VARIANT     267    267       P -> L (IN ADRP).
    FT                                /FTId=VAR_004825.
    FT   VARIANT     267    267       P -> R (IN ADRP).
    FT                                /FTId=VAR_004826.
    FT   VARIANT     292    292       A -> E (IN CSNB4).
    FT                                /FTId=VAR_004827.
    FT   VARIANT     296    296       K -> E (IN ADRP).
    FT                                /FTId=VAR_004828.
    FT   VARIANT     297    297       S -> R (IN ADRP).
    FT                                /FTId=VAR_004829.
    FT   VARIANT     342    342       T -> M (IN ADRP).
    FT                                /FTId=VAR_004830.
    FT   VARIANT     345    345       V -> L (IN ADRP).
    FT                                /FTId=VAR_004831.
    FT   VARIANT     345    345       V -> M (IN ADRP).
    FT                                /FTId=VAR_004832.
    FT   VARIANT     347    347       P -> A (IN ADRP).
    FT                                /FTId=VAR_004833.
    FT   VARIANT     347    347       P -> L (IN ADRP; COMMON VARIANT).
    FT                                /FTId=VAR_004834.
    FT   VARIANT     347    347       P -> Q (IN ADRP).
    FT                                /FTId=VAR_004835.
    FT   VARIANT     347    347       P -> R (IN ADRP).
    FT                                /FTId=VAR_004836.
    FT   VARIANT     347    347       P -> S (IN ADRP).
    FT                                /FTId=VAR_004837.
    SQ   SEQUENCE   348 AA;  38892 MW;  07443BEA CRC32;
         MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
         VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
         GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
         EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
         ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
         YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
    //

## Output file format

### Output files for usage example

### File: opsd_human.pscan

    CLASS 1
    Fingerprints with all elements in order

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

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

    CLASS 4
    Remaining partial matches

    Fingerprint GPCRRHODOPSN Elements 7
        Accession number PR00237
        Rhodopsin-like GPCR superfamily signature
      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

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

## 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
pestfind | Finds PEST motifs as potential proteolytic cleavage sites
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)

Alan Bleasby (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## History

## Target users

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

## Comments