THE SBASE DOMAIN LIBRARY - A COLLECTION OF ANNOTATED PROTEIN SEGMENTS

SBASE is a database of annotated protein domain sequences representing various structural, functional, ligand binding and topogenic segments of proteins. The current release of SBASE contains 27 211 entries whi ch are provided with standardized names in order to facilitate retriev al. SBASE is cross-referenced to the major protein and nucleic acid da tabanks as well as to the PROSITE catalog of protein sequence patterns [Bairoch,A. (1992) Nucleic Acids Res., 20, Suppl., 2013-2118]. SBASE can be used to establish domain homologies through database search usi ng programs such as FASTA [Lipman and Pearson (1985) Science, 227, 143 6-1441], FASTDB [Brutlag et al. (1990) Comp. Appl. Biosci., 6, 237-245 ] or BLAST3 [Altschul and Lipman (1990) Proc. Natl. Acad. Sci. USA, 87 , 5509-5513], which is especially useful in the case of loosely define d domain types for which efficient consensus patterns cannot be establ ished. The use of SBASE is illustrated on the DNA binding protein Brai n-4. The database and a set of search and retrieval tools are freely a vailable on request to the authors or by anonymous 'ftp' file transfer from <ftp.icgeb.tries.it>.