Swiss Institute Bioinformatics

The SWISS-PROT database [36] release 40.44 (February, 2003) contains over 120 000 sequences of proteins with more than 44 million amino adds abstracted from about 100 000 references. Besides sequence data, bibHographical references, and taxonomy data, there are highly valuable annotations of information (e.g., protein function), a minimal level of redundancy, and a high level of integration with other databases (EMBL, PDB, PIR, etc.). The database was initiated in 1987 by a partnership between the Department of Medicinal Biochemistry of the University of Geneva, Switzerland, and the EMBL. Now SWISS-PROT is driven as a joint project of the EMBL and the Swiss Institute of Bioinformatics (SIB). 

Swiss Prot EMBL and Swiss Institute of Bioinformatics protein sequence biblio., sub- stance, se- quence 120000 protein sequences, 44 mio amino adds journals, author submis- sions European Bioinformatics Institute free periodi- cally http //www.e- bi.ac.uk/swis- sprot/in- dex.html... 

The Swiss-Prot database is probably the most widely used protein database. It is maintained collaboratively by the European Bioinformatics Institute (EBI) and the Swiss Institute for Bioinformatics. It is relatively easy to access and search via the World Wide Web (Table 2.4). A sample entry for human insulin is provided in Figure 2.4. Additional information detailing such databases is available via the web addresses provided in Table 2.4 and in the bioinformatics publications listed at the end of this chapter. 

Guex, N., Diemand, A., Peitsch, M. C., and Schwede, T. Deep View Swiss Pdb Viewer. Basel Swiss Institute of Bioinformatics, 2001. Available on line at www.expasy.org/ spdbv/. 

SwissProt (http //www.expasy.org/sprot), database established by the Swiss Institute of Bioinformatics, provides protein sequences with high level of annotation. Highly integrated with other protein databases. All data are verified manually. 

SWISS-PROT (Bairoch and Apweiler, 1999) is an annotated protein sequence database established in 1986 and maintained collaboratively by the Swiss Institute of Bioinformatics and the EMBL Outstation, The European Bioinformatics Institute (EBI). It strives to provide a high level of annotation, a minimal level of redundancy, a high level of... 

CC This SWISS-PROT entry is copyright. It is produced CC through a Collaboration between the Swiss Institute of CC Bioinformatics and the EMBL outstation - the European CC Bioinformatics Institute. There are no restrictions on CC its use by non-profit institutions as long as its content CC is in no way modified and this statement is not removed. 

Proteomics server of the Swiss institute of bioinformatics. Dedicated to analysis of protein sequences and structure, as well as 2-D SDS-PAGE. 

SWISS-PROT (Bairoch and Apweiler, 2000) is a protein sequence database that, from its inception in 1986, was produced collaboratively by the Department of Medical Biochemistry at the University of Geneva and the EMBL. The database is now maintained collaboratively by Swiss Institute of Bioinformatics (SIB) and EBI/EMBL. SWISS-PROT provides high-level annotations, including descriptions of the function of the protein and of the structure of its domains, its post-translational modifications, its variants, and so on. The database can be accessed from http //expasy.hcuge.ch/sprot/sprot-top.html or numerous mirror sites. In 1966, Translated EMBL (TrEMBL) was created as a computer-annotated supplement to SWISS-PROT (Bleasby et al, 1994). 

HAMAP Swiss Institute of Bioinformatics Database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot (http //hamap.expasy.org/)... 

ExPASy is a database maintained by the Swiss Institute of Bioinformatics (SIB) that is dedicated to the organization of protein sequences. ISREC is a similar database maintained by the Bioinformatics Group... 

Universal Protein Knowledgebase (UniProt). European Bioinformatics Institute (EBI), Swiss Institute of Bioinformatics (SIB), Protein Information Resource (PIR), Georgetown Univ. URL http //www.uniprot.org. Central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. A central access point for extensive curated protein information, including function, classification, and cross-reference. 

Swiss Institute of Bioinformatics (SIB), Geneva, CH, M. Peitsch et al. http //guitar.rockefeller.edu/modeller/ modeller.html... 

PROSITE Database of sequence patterns and profile indicative for protein function http //www.expasy.org/prosite/ Swiss Institute of Bioinformatics (SIB), [86, 87]... 

The CMS Molecular Biology Resource [168] at the San Diego Supercomputer Center contains an excellent compendium of Web-accessible bioinformatics tools. The ExPASy (Expert Protein Analysis System] proteomics server of the Swiss Institute of Bioinformatics [169] and the EBI Toolbox are two other popular tool collections. Another useful resource is Herbert Mayer s Bioinformatics World Web site, which contains a comprehensive collection of bioinformatics tools and software, including evaluations, comments, and tutorials. 

The ENZYME database1501, maintained by the Swiss Institute for Bioinformatics (SIB), provides a comprehensive list of all IUBMB classifications, together with associated information such as systematic and alternative enzyme names, cofactor requirements, and pointers to the corresponding entry in the SWISS-PROT database of protein sequences1511. In addition, there is a concise free-text description of the reaction catalyzed, together with a description of preferential substrates and products. Currently, the ENZYME database holds entries for approximately 3700 enzymes. 

Swiss-Prot of Swiss Institute of Bioinformatics UniProt consortium ... 

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