The SBASE protein domain library, release 5.0: A collection of annotated protein sequence segments

Péter Fábián, Jänos Murvai, Zsolt Hâtsâgi, Kristian Vlahoviôek, Hedvig Hegyi, Sándor Pongor

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

SBASE 5.0 is the fifth release of SBASE, a collection of annotated protein domain sequences that represent various structural, functional, ligand-binding and topogenic segments of proteins. SBASE was designed to facilitate the detection of functional homologies and can be searched with standard database-search programs. The present release contains over 79,863 entries provided with standardized names and is cross-referenced to all major sequence databases and sequence pattern collections. The information is assigned to individual domains rather than to entire protein sequences, thus SBASE contains substantially more cross-references and links than do the protein sequence databases. The entries are clustered into > 16,000 groups in order to facilitate the detection of distant similarities. SBASE 5.0 is freely available by anonymous 'ftp' file transfer from <ftp.icgeb.trieste.it >. Automated searching of SBASE with BLAST can be carried out with the WWW-server <http://www.icgeb.trieste.it/sbase/ >. and with the electronic mail server <sbase@icgeb.trieste.it > which now also provides a graphic representation of the homologies. A related WWW-server <http://www.abc.hu/blast.html > and e-mail server <domain@hubi.abc.hu > predicts SBASE domain homologies on the basis of SWISS-PROT searches.

Original languageEnglish
Pages (from-to)240-243
Number of pages4
JournalNucleic acids research
Volume25
Issue number1
DOIs
Publication statusPublished - Jan 1 1997

ASJC Scopus subject areas

  • Genetics

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