PRINTS and PRINTS-S shed light on protein ancestry

The PRINTS database houses a collection of protein fingerprints. These may be used to make family and tentative functional assignments for uncharacterised sequences. The September 2001 release (version 32.0) includes 1600 fingerprints, encoding approximately 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 conventional sequence analysis approaches. The database is accessible for BLAST, fingerprint and text searches at http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/.

[1]  Shmuel Pietrokovski,et al.  Increased coverage of protein families with the Blocks Database servers , 2000, Nucleic Acids Res..

[2]  Douglas L. Brutlag,et al.  The EMOTIF database , 2001, Nucleic Acids Res..

[3]  Alex Bateman,et al.  The InterPro database, an integrated documentation resource for protein families, domains and functional sites , 2001, Nucleic Acids Res..

[4]  Terri K. Attwood,et al.  PRINTS prepares for the new millennium , 1999, Nucleic Acids Res..

[5]  T K Attwood,et al.  A compendium of specific motifs for diagnosing GPCR subtypes. , 2001, Trends in pharmacological sciences.

[6]  Terri K. Attwood,et al.  PRECIS: Protein reports engineered from concise information in SWISS-PROT , 2003, Bioinform..

[7]  Robert D. Finn,et al.  The Pfam protein families database , 2004, Nucleic Acids Res..

[8]  Terri K. Attwood,et al.  BLAST PRINTS - alternative perspectives on sequence similarity , 1999, Bioinform..

[9]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[10]  Terri K. Attwood,et al.  PRINTS-S: the database formerly known as PRINTS , 2000, Nucleic Acids Res..

[11]  Jérôme Gouzy,et al.  ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons , 2000, Nucleic Acids Res..

[12]  Amos Bairoch,et al.  The PROSITE database, its status in 2002 , 2002, Nucleic Acids Res..

[13]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..

[14]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[15]  B. Rost,et al.  Marrying structure and genomics. , 1998, Structure.

[16]  Amos Bairoch,et al.  The PROSITE database, its status in 1997 , 1997, Nucleic Acids Res..

[17]  Ulf Leser,et al.  EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation , 1999, German Conference on Bioinformatics.

[18]  Amos Bairoch,et al.  The PROSITE database, its status in 1999 , 1999, Nucleic Acids Res..

[19]  Terri K. Attwood,et al.  FingerPRINTScan: intelligent searching of the PRINTS motif database , 1999, Bioinform..