pscan

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Function

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

% 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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1)	seqall	Protein sequence(s) filename and optional format, or reference (input USA)	Readable sequence(s)	Required
-emin	integer	Minimum number of elements per fingerprint	Integer from 1 to 20	2
-emax	integer	Maximum number of elements per fingerprint	Integer up to 20	20
[-outfile] (Parameter 2)	outfile	Output file name	Output file	<*>.pscan
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1 -sbegin_sequence	integer	Start of each sequence to be used	Any integer value	0
-send1 -send_sequence	integer	End of each sequence to be used	Any integer value	0
-sreverse1 -sreverse_sequence	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask1 -sask_sequence	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide1 -snucleotide_sequence	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein1 -sprotein_sequence	boolean	Sequence is protein	Boolean value Yes/No	N
-slower1 -slower_sequence	boolean	Make lower case	Boolean value Yes/No	N
-supper1 -supper_sequence	boolean	Make upper case	Boolean value Yes/No	N
-scircular1 -scircular_sequence	boolean	Sequence is circular	Boolean value Yes/No	N
-squick1 -squick_sequence	boolean	Read id and sequence only	Boolean value Yes/No	N
-sformat1 -sformat_sequence	string	Input sequence format	Any string
-iquery1 -iquery_sequence	string	Input query fields or ID list	Any string
-ioffset1 -ioffset_sequence	integer	Input start position offset	Any integer value	0
-sdbname1 -sdbname_sequence	string	Database name	Any string
-sid1 -sid_sequence	string	Entryname	Any string
-ufo1 -ufo_sequence	string	UFO features	Any string
-fformat1 -fformat_sequence	string	Features format	Any string
-fopenfile1 -fopenfile_sequence	string	Features file name	Any string
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile	string	Output directory	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

Input file format

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

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

• prints.mat Matrices derived from PRINTS
• Pxxxxx Information for each fingerprint

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

"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

Known bugs

See also

• 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)

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

History

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