Scans proteins using PRINTS


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:


Here is a sample session with pscan

% pscan 
Scans proteins using PRINTS
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

   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
   -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 dying program messages

Standard (Mandatory) qualifiers Allowed values Default
(Parameter 1)
Protein sequence(s) filename and optional format, or reference (input 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
(Parameter 2)
Output file name Output file <*>.pscan
Additional (Optional) qualifiers Allowed values Default
Advanced (Unprompted) qualifiers Allowed values Default

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              Reviewed;         348 AA.
AC   P08100; Q16414; Q2M249;
DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1988, sequence version 1.
DT   20-MAR-2007, entry version 91.
DE   Rhodopsin (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]
RX   MEDLINE=84272729; PubMed=6589631;
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]
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]
RC   TISSUE=Retina;
RG   The German cDNA consortium;
RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN   [4]
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]
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.";
RL   Gene 167:317-320(1995).
RN   [6]
RX   MEDLINE=94004905; PubMed=8401533;
RA   Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
RA   Bhattacharya S.;

  [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).
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).
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).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (in RP4).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;

Output file format

Output files for usage example

File: opsd_human.pscan

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

All elements match but not all in the correct order

Not all elements match but those that do are in order

Remaining partial matches

The program reports hits in four classes.

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

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


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.


  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.


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
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


Alan Bleasby (ajb ©
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK


Target users

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