EMBOSS: pscan

pscan

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

Command line arguments

Input file format

pscan reads one or more protein sequence USAs.

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

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

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 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

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.