PRINTS

http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/

Attwood, T.K¹, Blythe, M.J.³, Flower, D.R.³, Gaulton, A.¹, Mabey, J.E.¹, Maudling, N.¹, McGregor, L.⁴, Mitchell, A.², Moulton, G.¹, Paine, K.³, Scordis, P.¹

¹School of Biological Sciences University of Manchester Manchester M13 9PT, UK
²EMBL Outstation - EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
³Edward Jenner Institute for Vaccine Research Compton, Newbury Berkshire RG20 7NN, UK
⁴INSERM Unit 331 Faculty of Medicine R.T.H.Laennec Rue G.Paradin, 69372 Lyon, cedex08, France

Contact attwood@bioinf.man.ac.uk

Database Description

The PRINTS database houses a collection of protein family fingerprints. These may be used to make family and tentative functional assignments for uncharacterised sequences. The September 2002 release (version 32.0) includes around 1660 fingerprints, encoding ~10,000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. In addition to its continued steady growth, we report here its use as a source of annotation in the InterPro resource, and the use of its relational cousin, PRINTS-S, to model relationships between families, including those beyond the reach of conventioal sequence analysis approaches.. The database is accessible for BLAST, fingerprint and text searches at http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/.

Recent Developments

We have developed an automatic supplement to PRINTS, termed prePRINTS, which is helping to increase the family coverage of PRINTS and so improve its effectiveness as a sequence analysis tool. An essential component of this resource is PRECIS (Protein Reports Engineered from Concise Information in SWISS-PROT), which allows us to generate family annotation fully automatically.

Acknowledgements

PRINTS is built and maintained at the University of Manchester with support from the Royal Society (TKA is a Royal Society University Research Fellow). We are grateful for individual support from the MRC (AG), the BBSRC (AM), the EPSRC (NM), Biofocus (GM), CIGMR (AU) and the EC (PB).

REFERENCES

1. Attwood, T.K., Blythe, M., Flower, D.R., Gaulton, A., Mabey, J.E., Maudling, N.,
McGregor, L., Mitchell, A., Moulton, G., Paine, K. and Scordis, P. (2002) PRINTS and PRINTS-S shed light on protein ancestry. Nucleic Acids Res., 30, 239-241.
2. Attwood, T.K. (2001) A compendium of specific
motifs for diagnosing GPCR subtypes. Trends Pharmacological Sci., 22, 162-165.
3. Attwood, T.K., Croning, M.D.R., Flower, D.R.,
Lewis, A.P., Mabey, J.E., Scordis, P., Selley, J.
and Wright, W. (2000) PRINTS-S: the database
formerly known as PRINTS. Nucleic Acids Res., 28,
225-227.
4. Wright, W., Scordis, P. and Attwood, T.K. (1999) BLAST PRINTS - An alternative perspective on sequence similarity. Bioinformatics, 15, 523-524.
5. Scordis, P., Flower, D.R. and Attwood, T.K. (1999) FingerPRINTScan: Intelligent searching of
the PRINTS motif database. Bioinformatics, 15, 799
-806.
6. Apweiler R., Attwood, T.K., Bairoch A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L, Corpet, F., Croning, M.D.R., Durbin, R.,Falquet, L., Fleischmann, W., Gouzy, J., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A., Karavidopoulou, Y., Lopez, R., Marx, B., Mulder, N. J., Oinn, T.M., Pagni, M., Servant, F., Sigrist, C. J. A. and Zdobnov, E. M. (2001) The InterPro database, an integrated documentation
resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.