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 protein 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

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
   -emin               integer    [2] Minimum number of elements per
                                  fingerprint (Integer from 1 to 20)
   -emax               integer    [20] Maximum number of elements per
                                  fingerprint (Integer up to 20)
  [-outfile]           outfile    [*.pscan] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -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
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated 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 standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -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 dying program messages

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              Reviewed;         348 AA.
AC   P08100; Q16414; Q2M249;
DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1988, sequence version 1.
DT   20-MAR-2007, entry version 91.
DE   Rhodopsin (Opsin-2).
GN   Name=RHO; Synonyms=OPN2;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=84272729; PubMed=6589631;
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   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
RA   Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
RT   "Genome-wide discovery and analysis of human seven transmembrane helix
RT   receptor genes.";
RL   Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Retina;
RG   The German cDNA consortium;
RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
RX   PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
RA   Bennett J., Beller B., Sun D., Kariko K.;
RT   "Sequence analysis of the 5.34-kb 5' flanking region of the human
RT   rhodopsin-encoding gene.";
RL   Gene 167:317-320(1995).
RN   [6]
RP   REVIEW ON RP4 VARIANTS.
RX   MEDLINE=94004905; PubMed=8401533;
RA   Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
RA   Bhattacharya S.;


  [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 RP4).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -> R (in RP4).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -> K (in RP4).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -> C (in RP4).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -> R (in RP4).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       Missing (in RP4).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       Missing (in RP4).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -> L (in RP4).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -> R (in RP4).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -> E (in CSNBAD1).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -> E (in RP4).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -> R (in RP4).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -> M (in RP4).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -> L (in RP4).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -> M (in RP4).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -> A (in RP4).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -> L (in RP4; common variant).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -> Q (in RP4).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -> R (in RP4).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (in RP4).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;
     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

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



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



CLASS 4
Remaining partial matches

   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
   epestfind      Finds PEST motifs as potential proteolytic cleavage sites
   fuzzpro        Protein pattern search
   fuzztran       Protein pattern search after translation
   helixturnhelix Report nucleic acid binding motifs
   oddcomp        Find 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)

   Alan Bleasby (ajb  ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

Target users

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

Comments

   None