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This compendium of protein sequence alignments is a companion resource to
the PRINTS database of protein fingerprints [1,2]. For each entry in PRINTS,
we have made available a corresponding alignment in NBRF/PIR format: the
root name of each of these is identical to the PRINTS identification code.
Fingerprints are derived from groups of conserved motifs in multiple alignments.
These are used to dredge a SWISS-PROT/TrEMBL composite database [3,4] in an
iterative fashion, so the fingerprints mature with each database pass [5-7]
- further details of the nature and derivation of fingerprints are given
in the PRINTS readme and documentation files.
Disclaimer
----------
The alignments are, in the main, only intended to be reliable in the regions
from which fingerprints have been defined, although many are complete over the
full sequence length. Each has been generated manually, using either SOMAP [8]
(part of the ADSP suite [5]), XALIGN/VISTAS [9] or CINEMA [10]. We make no
claims for their `correctness' (if such a thing exists), but provide them in
good faith as a guide to, or as an illustration of, the type of protein families
contained in PRINTS. We hope they will be of use to those wishing to augment the
information in PRINTS, or to others who simply seek a convenient starting point
for their own analyses - the files should be accessible to any software that
reads NBRF/PIR format.
CINEMA is accessible from http://www.bioinf.man.ac.uk/dbbrowser/CINEMA2.1/
References
----------
1. Attwood, T.K. and Beck, M.E. (1994) PRINTS - A protein motif fingerprint
database. Protein Engineering, 7 (7), 841-848.
2. Attwood, T.K., Bleasby, A.J., Beck, M.E. and Parry-Smith, D.J. (1994) PRINTS
- A database of protein motif fingerprints. Nucleic Acids Res., 22 (17),
3590-3596.
3. Bleasby, A.J. and Wootton, J.C. (1990) Constructing validated, non-
redundant composite protein sequence databases. Protein Engineering, 3 (3),
153-159.
4. Bleasby, A.J., Akrigg, D. and Attwood, T.K. (1994) OWL - A non-redundant,
composite protein sequence database. Nucleic Acids Res., 22 (17), 3574-3577.
5. Parry-Smith, D.J. and Attwood, T.K. (1992) ADSP - A new package for
computational sequence analysis. CABIOS, 8 (5), 451-459.
6. Attwood, T.K. and Findlay, J.B.C. (1994) Fingerprinting G-protein-coupled
receptors. Prot.Engng. 7 (2), 195-203.
7. 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.
8. Parry-Smith, D.J. and Attwood, T.K. (1991) SOMAP - A novel interactive
approach to multiple protein sequence aligment. CABIOS, 7 (2), 233-235.
9. Perkins, D.N. and Attwood, T.K. VISTAS - A package for VIsualising
STructures And Sequences. J.Mol.Graph., 13, 73-75.
10. 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.
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