                                    pscan



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Scan protein sequence(s) with fingerprints from the PRINTS database

Description

   pscan reads one or more protein sequences and searches them against the
   PRINTS database of diagnostic protein signatures (fingerprints). A
   fingerprint is a group of conserved motifs or elements that together
   form a diagnostic signature for a particular protein family. The
   minimum and maximum number of elements per fingerprint may be
   specified. pscan writes an output file with details of any matches
   between each input sequence and the fingerprints. 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.

Algorithm

   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 a PRINTS alignment. Each matrix therefore has a highest
   possible score, being the sum of the maximum score of each column. A
   match to a window over the input sequence 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.

Usage

   Here is a sample session with pscan


% pscan
Scan protein sequence(s) with fingerprints from the PRINTS database
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

Scan protein sequence(s) with fingerprints from the PRINTS database
Version: EMBOSS:6.6.0.0

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   pscan reads one or more protein sequences.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  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   13-JUN-2012, entry version 145.
DE   RecName: Full=Rhodopsin;
DE   AltName: Full=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; DOI=10.1073/pnas.81.15.4851;
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;
RX   PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA   Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA   Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H.,
RA   Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K.,
RA   Ottenwaelder B., Poustka A., Wiemann S., Schupp I.;
RT   "The full-ORF clone resource of the German cDNA consortium.";
RL   BMC Genomics 8:399-399(2007).
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.";


  [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; dbSNP:rs28933993).
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; dbSNP:rs29001653).
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; dbSNP:rs29001566).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (in RP4; dbSNP:rs29001637).
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

   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.

   The home web page of the PRINTS database is:
   http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/

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 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.

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        Find antigenic sites in proteins
   epestfind        Find PEST motifs as potential proteolytic cleavage sites
   fuzzpro          Search for patterns in protein sequences
   fuzztran         Search for patterns in protein sequences (translated)
   patmatdb         Search protein sequences with a sequence motif
   patmatmotifs     Scan a protein sequence with motifs from the PROSITE
                    database
   preg             Regular expression search of protein sequence(s)
   sigcleave        Report on signal cleavage sites in a protein sequence

     * 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
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

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

Comments

   None
