THE SBASE PROTEIN DOMAIN LIBRARY, RELEASE 3.0 - A COLLECTION OF ANNOTATED PROTEIN-SEQUENCE SEGMENTS

SBASE 3.0 is the third release of SBASE, a collection of annotated pro tein domain sequences. SBASE entries represent various structural, fun ctional, ligand-binding and topogenic segments of proteins as defined by their publishing authors. SBASE can be used for establishing domain homologies using different database-search tools such as FASTA [Lipma n and Pearson (1985) Science, 227, 1436-1441], and BLAST3 [Altschul an d Lipman (1990) Proc. Natl. Acad. Sci. USA, 87, 5509-5513] which is es pecially useful in the case of loosely defined domain types for which efficient consensus patterns can not be established. The present relea se contains 41,749 entries provided with standardized names and cross- referenced to the major protein and nucleic acid databanks as well as to the PROSITE catalogue of protein sequence patterns. The entries are clustered into 2285 groups using the BLAST algorithm for computing si milarity measures. SBASE 3.0 is freely available on request to the aut hors or by anonymous 'ftp' file transfer from [ftp.icgeb.trieste.it]. Individual records can be retrieved with the gopher server at [icgeb.t rieste.it] and with a www-server at [http://www.icgeb.trieste.it]. Aut omated searching of SBASE by BLAST can be carried out with the electro nic mail server [sbase @ icgeb.trieste.it]. Another mail server [domai n @ hubi.abc.hu] assigns SBASE domain homologies on the basis of SWISS -PROT searches. A comparison of pertinent search strategies is present ed.