UNLABELLED: The Protein Information Resource (PIR) has greatly expanded its Web site and developed a set of interactive search and analysis tools to facilitate the analysis, annotation, and functional identification of proteins. New search engines have been implemented to combine sequence similarity search results with database annotation information. The new PIR search systems have proved very useful in providing enriched functional annotation of protein sequences, determining protein superfamily-domain relationships, and detecting annotation errors in genomic database archives. AVAILABILITY: http://pir.georgetown.edu/. CONTACT: [email protected]

MOTIVATION: The Protein Information Resource (PIR) maintains a database of annotated and curated alignments in order to visually represent interrelationships among sequences in the PIR-International Protein Sequence Database, to spread and standardize protein names, features and keywords among members of a family or superfamily, and to aid us in classifying sequences, in identifying conserved regions, and in defining new homology domains. RESULTS: Release 22.0, (December 1998), of the PIR-ALN database contains a total of 3806 alignments, including 1303 superfamily, 2131 family and 372 homology domain alignments. This is an appropriate dataset to develop and extract patterns, test profiles, train neural networks or build Hidden Markov Models (HMMs). These alignments can be used to standardize and spread annotation to newer members by homology, as well as to understand the modular architecture of multidomain proteins. PIR-ALN includes 529 alignments that can be used to develop patterns not represented in PROSITE, Blocks, PRINTS and Pfam databases. The ATLAS information retrieval system can be used to browse and query the PIR-ALN alignments. AVAILABILITY: PIR-ALN is currently being distributed as a single ASCII text file along with the title, member, species, superfamily and keyword indexes. The quarterly and weekly updates can be accessed via the WWW at pir.georgetown.edu. The quarterly updates can also be obtained by anonymous FTP from the PIR FTP site at NBRF.Georgetown.edu, directory [ANONYMOUS.PIR.ALIGNMENT].