Swiss-PROT databases

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). 

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. 

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

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/...

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

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

R. Apweiler, H. Hermjakob, and N. Sharon, On the frequency of protein glycosy-lation, as deduced from analysis of the SWISS-PROT database, Biochim. Biophys. Acta 1473 (1999), 4-8. 

The output from these applications themselves forms a database and often contains information related to entries in other databases. For example, if a BLAST run is performed against the SWISS-PROT database then the output will contain SWISS-PROT accession numbers and parts of se-... 

Below (Figure 1.15) is a perl script for searching the SWISS-PROT database for the entry with ID C931 SOYBN . A set of entries is returned, this time with just one entry in it. The entry can be retrieved using the getEntry method of the set class, and the fieldToString method of the entry class is... 

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. 

Non-redundant merge of SWISS-PROT, PIR, PRF, and proteins derived from GenBank coding sequences and PDB atomic coordinates Subset of nr which is new or modified within the last 30 days The SWISS-PROT database... 

For each reaction in the generated pathway, users can manually select the reactions to be represented by dynamic equations. InitiaUy, the GEM system would automatically search for static reactions based on monomer enzymes found in Brenda and Swiss-PROT databases. Based on the search results, the static part of the model is then generated using the hybrid dynamic/static simulation algorithm detailed below. Finally, the generated pathway model can be used for simulations in E-Ccll System. Users can then specify dynamic equations by selecting an appropriate reaction mechanism and input reaction parameters, or they can program their own set of reaction process description files. 

Figure 10. Histograms of the median score for the E. coli scan. (A) shows the median score resulting from matches ofcdl E. coli proteins in the SWISS-PROT database, whereas (B) shows the average score of matches of all mouse proteins in SWISS-PROT. The matches in (B) provide a statistic for false matches, since the E. coli and mouse databases have a similar size (4602 and4066 entries, respectively). The vertical lines mark the 95% confidence...

Swiss-Prot and TrEMBL are the initial databases one would use to find information regarding the protein s sequence. Depending on the level of refinement and information provided for each sequence, data are deposited into either Swiss-Prot or TrEMBL. Because of the large number of sequences that are now determined from genomics alone, all sequences are first deposited into TrEMBL. Once the correct nomenclature, links to relevant databases, and significant comments are added, and after unnecessary information has been removed, the sequence is added to the Swiss-Prot database. The initial search for a sequence is typically performed on the information contained in these two databases. 

---