EMBOSS: pscan


Program 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:

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): sw:OPSD_HUMAN
Minimum number of elements per fingerprint [2]: 
Maximum number of elements per fingerprint [20]: 
Output file [opsd_human.pscan]:
%

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)

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

The input sequence can be one or more protein sequences.

Output file format

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
Here is part of a sample output:

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

Fingerprint RHODOPSIN Elements 6
    Accession number PR00579
    Rhodopsin signature
  Element 1 Threshold 80% Score 96%
             Start position 3 Length 19
  Element 2 Threshold 76% Score 100%
             Start position 22 Length 17
  Element 3 Threshold 53% Score 92%
             Start position 85 Length 17
  Element 4 Threshold 71% Score 100%
             Start position 191 Length 17
  Element 5 Threshold 56% Score 99%
             Start position 271 Length 19
  Element 6 Threshold 81% Score 93%
             Start position 319 Length 14


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

Fingerprint PROFILIN Elements 6
    Accession number PR00392
    Profilin signature
  Element 6 Threshold 31% Score 31%
             Start position 18 Length 18
  Element 6 Threshold 37% Score 37%
             Start position 318 Length 15


CLASS 4
Remaining partial matches

Fingerprint NANEUSMPORT Elements 8
    Accession number PR00176
    Sodium/chloride neurotransmitter symporter signature
  Element 2 Threshold 47% Score 47%
             Start position 38 Length 20

Data files

The data file is stored in the PRINTS directory of the standard EMBOSS data directory. 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 nameDescription
antigenicFinds antigenic sites in proteins
diffseqFind differences (SNPs) between nearly identical sequences
dotmatcherDisplays a thresholded dotplot of two sequences
dotpathDisplays a non-overlapping wordmatch dotplot of two sequences
dottupDisplays a wordmatch dotplot of two sequences
dregregular expression search of a nucleotide sequence
fuzznucNucleic acid pattern search
fuzzproProtein pattern search
fuzztranProtein pattern search after translation
garnierPredicts protein secondary structure
helixturnhelixReport nucleic acid binding motifs
oddcompFinds protein sequence regions with a biased composition
patmatdbSearch a protein sequence with a motif
patmatmotifsSearch a PROSITE motif database with a protein sequence
pepcoilPredicts coiled coil regions
polydotDisplays all-against-all dotplots of a set of sequences
pregregular expression search of a protein sequence
printsextractExtract data from PRINTS
prosextractBuilds the PROSITE motif database for patmatmotifs to search
showseqDisplay a sequence with features, translation etc
sigcleaveReports protein signal cleavage sites
tfscanScans DNA sequences for transcription factors
tmapDisplays membrane spanning regions

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Target users

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

Comments