SWISS database

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, TrEMBL Annotated non-redundant protein sequence database, TrEMBL is a computer-annotated supplement to Swiss-Prot. TrEMBL contains the translations of all coding sequences present in the EMBL Nucleotide Sequence Database which are no yet integrated into Swiss-Prot... 

Data-Star. This is Europe s leading on-line database service (39) and covers worldwide business news, financial information, market research, trade statistics, business analysis, healthcare / pharmaceuticals, chemicals / petrochemicals, chemical industry, biomedicine /life science, biotechnology, and technology, with an emphasis on Europe. It was originally formed as a joint venture among BRS, Predicasts, and Radio Suisse (the Swiss telecommunications company) (37). Data-Star offers access to about 300 bibliographic, abstract, directory, and fuU-text on-line databases, of which approximately 150 are also available on Dialog (40). 

Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28 45-48... 

Maintains the EMBL Nucleotide and SWISS-PROT databases as well as other databases.)... 

Upon alignment of 25 endo- and exo-polygalacturonases taken from the swiss.prot. database only one histidine appeared to be conserved throughout. The conserved histidine at position 223 in PGII was changed into alanine, a small apolar residue. 

Ecoinvent database by Frischknecht et al. (2006) v.1.3. Swiss Centre for Life Cycle Inventories, Switzerland. 

Bacterial proteins from MALDI FTMS experiments are identifiable using the Swiss-Prot database.53 In order to identify any microorganism, it is neces-... 

Recently, there has been great interest in proteins that exhibit biological activity but lack a well-defined secondary or tertiary structure after purification (Dunker et al., 1998, 2001 Schweers et al., 1994 Uversky et al., 2000 Wright and Dyson, 1999). Such proteins are referred to as intrinsically disordered or unstructured. An analysis in 1998 of the Swiss Protein Database revealed that about 15,000 proteins in that database are likely to contain disordered segments at least 40 residues in length (Romero et al., 1998). Dyson and Wright (2002) review intrinsically disordered proteins in this volume. 

FIGURE 1.1 A 2D-gel electrophoresis map of colorectal epithelia cells proteins from the SWISS- 2DPage database (entry CATD HUMAN, primary access number P07339) accessible from http //www.expasy.org/swiss-2dpage. 

Moreover, experimental reference maps of human tissues were studied p7 and Mr coordinates of identified spots were retrieved from the SWISS-2D-PAGE database, the values <3X = 0.009 pH and av = 0.0002 log Mr were assumed for spot dimension since they represent the standard case for experimental 2D-PAGE maps—normal sample loading of a tissue homogenate (ca. 1 mg total protein) and standard gel sizes (18 x 20 cm, IEF x SDS-PAGE). 

Demalte-Annessi, I., Sanchez, J.-C., Hoogland, C., Rouge, V., Binz, P.-A., Appel, R.D., Hochstrasser, D.F. (1999). Submitted to the SWISS-2D-PAGE database. 

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. 

Figure 2.4 Sample entry for human insulin as present in the Swiss-Prot database. Refer to text for further details. Reproduced from the Swiss-Prot database on the Uniprot website htt //www.ebi.uniprot.org/...

GPCR and transporter protein information from SWISS-PROT has been imported as background data into the Arcadia database. This background information is used in Arcadia to simplify mutant submissions (wild-type proteins are already in the database and therefore do not have to be added by the user residue positions of the mutations... 

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. 

The protein sequence databases are the most comprehensive source of information on proteins. The goal of this chapter is to describe the different protein sequence databases available to researchers. It is necessary to distinguish between universal databases that cover proteins from all species and specialized data collections that store information about specific families or groups of proteins, or about the proteins of a specific organism. Two categories of universal protein sequence databases can be discerned simple archives of sequence data and annotated databases in which additional information has been added to the sequence record. The next section describes the Protein Information Resource (PIR), the oldest protein sequence database SWISS-PROT, an annotated universal sequence database and TrEMBL, the supplement of... 

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... 

The next lines, the OS (Organism Species) and OC (Organism Classification), describe the species from which the protein has been derived. The OS line shows the scientific name of the organism and, if existing, the common English name. The OC lines give the taxonomic tree. SWISS-PROT, as well as the DDBJ/EMBL/GenBank nucleotide sequence databases, uses the NCBI taxonomy to standardize the taxonomies of the molecular sequence databases. 

To return to the scientific content of the SWISS-PROT database, the next section contains the DR (Database cross-References) lines ... 

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