EMBOSS: pscan manual

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

   Standard (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

   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 deaths

Standard (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
Additional (Optional) qualifiers		Allowed values	Default
(none)
Advanced (Unprompted) 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

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

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.
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.
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.
Attwood, T.K. and Beck, M.E. (1994) PRINTS - A protein motif fingerprint database. Protein Engineering, 7(7), 841-848.
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.
Bleasby, A.J. and Wootton, J.C. (1990) Constructing validated, non- redundant composite protein sequence databases. Protein Engineering, 3(3), 153-159.
Parry-Smith, D.J. and Attwood, T.K. (1992) ADSP - A new package for computational sequence analysis. CABIOS, 8(5), 451-459.
Attwood, T.K. and Findlay, J.B.C. (1994) Fingerprinting G-protein-coupled receptors. Prot.Engng. 7(2), 195-203.
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.
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.
Parry-Smith, D.J. and Attwood, T.K. (1991) SOMAP - A novel interactive approach to multiple protein sequence aligment. CABIOS, 7(2), 233-235.
Perkins, D.N. and Attwood, T.K. (1995) VISTAS - A package for VIsualising STructures And Sequences of proteins. J.Mol.Graph., 13, 73-75.
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

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

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