Bioinformatics: PIR Database

Bioinformatics: PIR Database

The Protein Information Resource (PIR) is a major player in Bioinformatics field (Proteomics). It is a joint effort between Georgetown University Medical Centre and the National Biomedical Research Foundation in Washington, D.C.

It was established in 1984 and resulted from the work of Dr. Margaret Dayhoff. Her Atlas of Protein Sequence and Structure, published from 1965–1978, was the first comprehensive collection of protein sequences.

In 1974, Dr.Dayhoff devised the concept of the protein family and superfamily, defined by sequence similarity, as a means of organising and classifying proteins.

In recent years, this concept has been exploited by the PIR Protein Sequence Database (PIR-PSD) to enable them to computer-annotate their entries with functional and structural data. This has facilitated an increase in the number of sequences in the database.

There are many other Databases provided by PIR:

1- PIR-PSD: it has been the most comprehensive and expertly-curated protein sequence database in the public domain for over 20 years. In 2002, PIR joined EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics) to form the UniProt consortium. PIR-PSD sequences and annotations have been integrated into UniProt Knowledgebase.

2- IProClass: integrated resource of family relationships and structural and functional features of proteins. The iProClass database provides value-added information reports for UniProtKB and unique NCBI Entrez protein sequences in UniParc, with links to over 90 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genomes, ontologies, literature, and taxonomy.

3- The comprehensive PIR-NREF database of protein sequences: from PIR-PSD, Swiss-Prot, TrEMBL, RefSeq, GenPept, and PDB. PIR-NREF has been discontinued inasmuch as the UniProt databases now include all of its functionalities (Final Release 1.83, 16-Jan-2006). This consolidation provides one centralized comprehensive database and minimizes duplication of work between UniProt and PIR.

4- PIRSF: The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains.

To access the PIR Database click HERE

For more informations about Protein Databases, read THIS POST.

For more informations about the SwissProt Database, read THIS POST.

Read THIS POST to learn how to use the SwissProt Database.

Any questions you're welcome.